Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 192 of 202
Found at i:58518484 original size:17 final size:17
Alignment explanation
Indices: 58518432--58518486 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
58518422 ACATTTATTG
**
58518432 TTTATTATATTATTGAAT
1 TTTATTAT-TTATAAAAT
*
58518450 TTT-TCATTT-TAAATAT
1 TTTATTATTTATAAA-AT
58518466 TTTATTATTTATAAAAT
1 TTTATTATTTATAAAAT
58518483 TTTA
1 TTTA
58518487 ATTTACGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 2 0.07
16 7 0.23
17 14 0.47
18 7 0.23
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTATTATTTATAAAAT
Found at i:58519632 original size:8 final size:8
Alignment explanation
Indices: 58519621--58519649 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
58519611 TATATTATAT
58519621 TATTTTAA
1 TATTTTAA
58519629 TA-TTTAA
1 TATTTTAA
58519636 TATTTTAA
1 TATTTTAA
58519644 TATTTT
1 TATTTT
58519650 TTATTTATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATTTTAA
Found at i:58519633 original size:22 final size:22
Alignment explanation
Indices: 58519605--58519657 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
58519595 TTTTTTTAAA
*
58519605 AATATTTATATTATATTATTTT
1 AATATTTATATTATAATATTTT
*
58519627 AATATTTAATATTTTAATATTTT
1 AATATTT-ATATTATAATATTTT
*
58519650 -TTATTTAT
1 AATATTTAT
58519658 CGAAAGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 12 0.44
23 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATATTTATATTATAATATTTT
Found at i:58519654 original size:15 final size:15
Alignment explanation
Indices: 58519612--58519655 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
58519602 AAAAATATTT
58519612 ATATTATATTATTTTA
1 ATATT-TATTATTTTA
*
58519628 ATATTTAATATTTTA
1 ATATTTATTATTTTA
*
58519643 ATATTTTTTATTT
1 ATATTTATTATTT
58519656 ATCGAAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATATTTATTATTTTA
Found at i:58530214 original size:77 final size:75
Alignment explanation
Indices: 58530070--58530214 Score: 166
Period size: 77 Copynumber: 1.9 Consensus size: 75
58530060 AAATAATAGG
* * *
58530070 AAAAGACAAAAAATACCCTTGAGTTAATATTTATTATTTTGCAAAAGTAAGGGTATTTTAGTACT
1 AAAAGAAAAAAAATACCCTTGAGTTAATATTTATTACTTTGCAAAAGTAAGGGTATTTTAATACT
58530135 TTCTCATCTA
66 TTCTCATCTA
* * * * * *
58530145 AAAAGAAAAAAAGATACTCTTTATGTTAATATTTGTTACTTTGTAAAATTACA-TGTATTTTAAT
1 AAAAGAAAAAAA-ATACCCTTGA-GTTAATATTTATTACTTTGCAAAAGTA-AGGGTATTTTAAT
*
58530209 GCTTTC
63 ACTTTC
58530215 ATAACTGGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
75 11 0.19
76 8 0.14
77 37 0.65
78 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (75 bp):
AAAAGAAAAAAAATACCCTTGAGTTAATATTTATTACTTTGCAAAAGTAAGGGTATTTTAATACT
TTCTCATCTA
Found at i:58533945 original size:13 final size:13
Alignment explanation
Indices: 58533918--58533968 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
58533908 TTTGGCAATA
* *
58533918 CTTTTGAGAATTG
1 CTTTTGAAAAGTG
58533931 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
58533944 CTATGGAAAAGTG
1 CTTTTGAAAAGTG
58533957 CTTTTGAAAAGT
1 CTTTTGAAAAGT
58533969 TTAGTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:58535244 original size:16 final size:17
Alignment explanation
Indices: 58535215--58535247 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
58535205 CTCAAAAAAA
58535215 TAACACTAAAATTTATT
1 TAACACTAAAATTTATT
*
58535232 TAAC-CTAAGATTTATT
1 TAACACTAAAATTTATT
58535248 CTTTGCTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
TAACACTAAAATTTATT
Found at i:58535883 original size:2 final size:2
Alignment explanation
Indices: 58535876--58535902 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58535866 GAAATATGGC
58535876 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 A
58535903 AACTAGTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58536488 original size:15 final size:15
Alignment explanation
Indices: 58536445--58536491 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
58536435 AAGTTGTGGA
*
58536445 TTTAGTCTCTGTA-T
1 TTTAGTCTTTGTATT
*
58536459 TTTAAT-TTTGTTATT
1 TTTAGTCTTTG-TATT
58536474 TTTAGTCTTTGTATT
1 TTTAGTCTTTGTATT
58536489 TTT
1 TTT
58536492 TAAATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 13 0.48
16 4 0.15
ACGTcount: A:0.15, C:0.06, G:0.11, T:0.68
Consensus pattern (15 bp):
TTTAGTCTTTGTATT
Found at i:58539804 original size:18 final size:18
Alignment explanation
Indices: 58539767--58539815 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
58539757 TGAAATTATG
*
58539767 AAATATATAAA-ATCTTT
1 AAATATATAAATATATTT
*
58539784 AAATATATAAATTTATTT
1 AAATATATAAATATATTT
*
58539802 AAAAATATAAATAT
1 AAATATATAAATAT
58539816 TTATTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATATAAATATATTT
Found at i:58539824 original size:19 final size:20
Alignment explanation
Indices: 58539784--58539826 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
58539774 TAAAATCTTT
58539784 AAATATATAAATTTATTTAA
1 AAATATATAAATTTATTTAA
58539804 AAATATA-AATATTTA-TTAA
1 AAATATATAA-ATTTATTTAA
58539823 AAAT
1 AAAT
58539827 TAAGCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATATAAATTTATTTAA
Found at i:58540071 original size:17 final size:18
Alignment explanation
Indices: 58540041--58540078 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
58540031 TAAAAGGTTC
*
58540041 TAAAATAATATTAAA-AA
1 TAAAAAAATATTAAATAA
*
58540058 TAAAAAAATCTTAAATAA
1 TAAAAAAATATTAAATAA
58540076 TAA
1 TAA
58540079 TATAAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAAAATATTAAATAA
Found at i:58540254 original size:18 final size:17
Alignment explanation
Indices: 58540231--58540273 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
58540221 TTTTTTACAG
58540231 TATTTTTATA-AATTTATA
1 TATTTTTA-AGAATTT-TA
58540249 TATTTTTAAGAATTTTA
1 TATTTTTAAGAATTTTA
58540266 TAATTTTT
1 T-ATTTTT
58540274 TATTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATTTTTAAGAATTTTA
Found at i:58540255 original size:19 final size:18
Alignment explanation
Indices: 58540233--58540276 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
58540223 TTTTACAGTA
58540233 TTTTTATAAATTTATATAT
1 TTTTTATAAATTTATA-AT
* * *
58540252 TTTTAAGAATTTTATAAT
1 TTTTTATAAATTTATAAT
58540270 TTTTTAT
1 TTTTTAT
58540277 TAATATTTGC
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATAAATTTATAAT
Found at i:58541479 original size:108 final size:106
Alignment explanation
Indices: 58541292--58541496 Score: 322
Period size: 108 Copynumber: 1.9 Consensus size: 106
58541282 TGGATTAAGA
* * *
58541292 TTTAAGAGGATATTTGGCTATTTGGTCAGACGAGAAATCGAAACCCAGCACATTAGGGCACATTT
1 TTTAAAAGGATATTTGGCTATTTGATCAGACGAGAAATCAAAACCCAGCACATTAGGGCACATTT
*
58541357 TCTCGAATTTCCAAACACAAAACATTGCCTTACTTCGAAAT
66 TCTCGAATCTCCAAACACAAAACATTGCCTTACTTCGAAAT
*
58541398 TTTAAAAGGATATTTGGCTATTTGAT-AGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACG
1 TTTAAAAGGATATTTGGCTATTTGATCAG-ACGAG--AAATCAAAACCCAGCACATTAGGGCACA
*
58541462 TTTTCTCGAATCTCCAAACGCAAAACATTGCCTTA
63 TTTTCTCGAATCTCCAAACACAAAACATTGCCTTA
58541497 AAAAAATATT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
105 2 0.02
106 29 0.32
108 59 0.66
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGATCAGACGAGAAATCAAAACCCAGCACATTAGGGCACATTT
TCTCGAATCTCCAAACACAAAACATTGCCTTACTTCGAAAT
Found at i:58550679 original size:10 final size:10
Alignment explanation
Indices: 58550666--58550709 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
58550656 TTTATAGATA
58550666 TTATTTTAAT
1 TTATTTTAAT
58550676 TTATTTTAAT
1 TTATTTTAAT
*
58550686 ATAGATTTTAAT
1 -T-TATTTTAAT
*
58550698 ATATTTTAAT
1 TTATTTTAAT
58550708 TT
1 TT
58550710 TAAGCTTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 19 0.68
11 1 0.04
12 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TTATTTTAAT
Found at i:58562039 original size:366 final size:366
Alignment explanation
Indices: 58561304--58562773 Score: 2288
Period size: 366 Copynumber: 4.0 Consensus size: 366
58561294 AGCTCTAACA
* * * *
58561304 GTTGCAATTTCATGTTCAACTCGAGGAACTCCCTTTTG-TCCCATAACTGCCTCTGAAAGCACAT
1 GTTGCAGTTTCATGTTCAACTCGAGAAACTCCCTTTCGCT-CCATAACTGCCTCTGAAAGCGCAT
**** *
58561368 CAGAACTAACAACAGAAAGACAATCTGTGCTTCTCTTTGAATTAACCGGCTCCTGTGCACAAAAG
65 CAGAACTAACAACAGAAAGACAATCCACACTTCTCTTTGAATTAACCAGCTCCTGTGCACAAAAG
* *
58561433 TTGGCAACAACAGCGCTAGCAATGCTGCTGCTGCCCCACCGTTTTTTCCTCCTACTGTAAACTAA
130 TTGGCAACAACAGCGCTAGCACTGCTGCTGCTGCCCCACCGTTTCTTCCT-C--CTGTAAACTAA
* * *** *
58561498 AATCGGCATAGGACTTTCAAACATCACACTCGCAGATAACCAATGAGAACCAGTTTCGGGTAAGG
192 AATCGGCATAGGACTTTCAAACATCACACTCACAGATGACTGCTGAGAACCAGTTTTGGGTAAGG
**
58561563 GAAGGCATGAATCCTCAGCCTCTTTACATCCAGGTTGTGAAGTACCATCACATTTAGGAGTCATC
257 GAAGGCATGAATCCTCAGCCTCTTTACATCCACTTTGTGAAGTACCATCACATTTAGGAGTCATC
* ** *
58561628 CGGAAAGTTTCATTATCAGACATCCAATCACATAAAGAAATCTTT
322 TGCCAAGTTTCATTACCAGACATCCAATCACATAAAGAAATCTTT
*
58561673 GTTGCAGTTTCATGTTCAACTTGAGAAACTCCCTTTCGCTCCATAACTGCCTCTGAAAGCGCATC
1 GTTGCAGTTTCATGTTCAACTCGAGAAACTCCCTTTCGCTCCATAACTGCCTCTGAAAGCGCATC
58561738 AGAACTAACAACAGAAAGACAATCCACACTTCTCTTTGAATTAACCAGCTCCTGTGCACAAAAGT
66 AGAACTAACAACAGAAAGACAATCCACACTTCTCTTTGAATTAACCAGCTCCTGTGCACAAAAGT
* * * *
58561803 TGGCAACAACAGCGTTAGCACTGCTGCTTCTGCCCCACCGTTTCTTCCTCCTGTAAATTAAATTC
131 TGGCAACAACAGCGCTAGCACTGCTGCTGCTGCCCCACCGTTTCTTCCTCCTGTAAACTAAAATC
* * * * *
58561868 GGAATAGGACTTTCAAACCTCATACTTACAGATGACTGCTGAGAACCAATTTTGGGTAAGGGAAG
196 GGCATAGGACTTTCAAACATCACACTCACAGATGACTGCTGAGAACCAGTTTTGGGTAAGGGAAG
58561933 GCATGAATCCTCAGCCTCTTTACATCCACTTTGTGAAGTACCATCACATTTAGGAGTCATCTTG-
261 GCATGAATCCTCAGCCTCTTTACATCCACTTTGTGAAGTACCATCACATTTAGGAGTCATC-TGC
58561997 CAAGTTTCATTACCAGACATCCAATCACATAAAGAAATCTTT
325 CAAGTTTCATTACCAGACATCCAATCACATAAAGAAATCTTT
*
58562039 GTTGCAGTTTCATGTTCAACTCGAGAAACTCCCTTTCGCT---TAACTGCCTCTGAAAGTGCATC
1 GTTGCAGTTTCATGTTCAACTCGAGAAACTCCCTTTCGCTCCATAACTGCCTCTGAAAGCGCATC
* *
58562101 AGAACTAACAACAGAAAGACAATCCGCACTTCTCTTTGAATTAA-CATGCTCCTGTGCATAAAAG
66 AGAACTAACAACAGAAAGACAATCCACACTTCTCTTTGAATTAACCA-GCTCCTGTGCACAAAAG
* * * *
58562165 TTGGCAACAACAGAGCTAGCGCTGCTGCTGCTGCCCCACCGTTTCTTCCCCCTACTGTAAACTGA
130 TTGGCAACAACAGCGCTAGCACTGCTGCTGCTGCCCCACCGTTTCTT---CCTCCTGTAAACTAA
* * *
58562230 AATCGGCATAGGACTTTCAAACATCACATTCACAGATGGCTGCTGAGAACCAGTTCTGGGTAAGG
192 AATCGGCATAGGACTTTCAAACATCACACTCACAGATGACTGCTGAGAACCAGTTTTGGGTAAGG
58562295 GAAGGCATGAATCCTCAGCCTCTTTACATCCAGC-TTGTGAAGTACCATCACATTTAGGAGTCAT
257 GAAGGCATGAATCCTCAGCCTCTTTACATCCA-CTTTGTGAAGTACCATCACATTTAGGAGTCAT
*
58562359 CTGCCAAGTTTCATTACCAGACATCCAATCACATAAAGAAGTCTTT
321 CTGCCAAGTTTCATTACCAGACATCCAATCACATAAAGAAATCTTT
* * * *
58562405 GTTGCAGTTTCATGTTCAACTCGAGAAACTCCCTTTTGCTCCATAACTGCTTCTGAAAGTGCATT
1 GTTGCAGTTTCATGTTCAACTCGAGAAACTCCCTTTCGCTCCATAACTGCCTCTGAAAGCGCATC
*
58562470 AGAACTAACAACAGAAAAACAATCCACACTTCTCTTTGAATTAACCAGCTCCTGTGCACAAAAGT
66 AGAACTAACAACAGAAAGACAATCCACACTTCTCTTTGAATTAACCAGCTCCTGTGCACAAAAGT
* *
58562535 TGGCAACAACAGCACTAGCACTGCTGCTGCAGCCCCACCGTTTCTTCCTCCTGTAAACTAAAATC
131 TGGCAACAACAGCGCTAGCACTGCTGCTGCTGCCCCACCGTTTCTTCCTCCTGTAAACTAAAATC
* * *
58562600 GGCATAGGACTTTCAAACATCATACTCACAGATGACTGTTGAGAACCAGTTTTGGGAAAGGGAAG
196 GGCATAGGACTTTCAAACATCACACTCACAGATGACTGCTGAGAACCAGTTTTGGGTAAGGGAAG
* * *
58562665 GCATGAATCCTCAGCCTCTTTACAACCACTTTGTGAAGTACCATCGCATTTAGGAGTCATCAGCC
261 GCATGAATCCTCAGCCTCTTTACATCCACTTTGTGAAGTACCATCACATTTAGGAGTCATCTGCC
58562730 AAGTTTCATTACCAGACATCCAATCACATAAAGAAATCTTT
326 AAGTTTCATTACCAGACATCCAATCACATAAAGAAATCTTT
58562771 GTT
1 GTT
58562774 TCCTGCATTC
Statistics
Matches: 1013, Mismatches: 75, Indels: 29
0.91 0.07 0.03
Matches are distributed among these distances:
362 2 0.00
363 123 0.12
365 3 0.00
366 595 0.59
367 2 0.00
368 1 0.00
369 284 0.28
370 3 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (366 bp):
GTTGCAGTTTCATGTTCAACTCGAGAAACTCCCTTTCGCTCCATAACTGCCTCTGAAAGCGCATC
AGAACTAACAACAGAAAGACAATCCACACTTCTCTTTGAATTAACCAGCTCCTGTGCACAAAAGT
TGGCAACAACAGCGCTAGCACTGCTGCTGCTGCCCCACCGTTTCTTCCTCCTGTAAACTAAAATC
GGCATAGGACTTTCAAACATCACACTCACAGATGACTGCTGAGAACCAGTTTTGGGTAAGGGAAG
GCATGAATCCTCAGCCTCTTTACATCCACTTTGTGAAGTACCATCACATTTAGGAGTCATCTGCC
AAGTTTCATTACCAGACATCCAATCACATAAAGAAATCTTT
Found at i:58562985 original size:127 final size:127
Alignment explanation
Indices: 58562761--58563137 Score: 688
Period size: 127 Copynumber: 3.0 Consensus size: 127
58562751 AATCACATAA
58562761 AGAAATCTTTGTTTCCTGCATTCAAACACAT--AATAGGACTGTTTCAATTGAACTAGAAATTTG
1 AGAAATCTTTGTTTCCTGCATTCAAACACATAAAATAGGACTGTTTCAATTGAACTAGAAATTTG
58562824 AAGTCCCAATCTAAATCTCACCTAATATAATTCAACAAACACAAAATCAGGGTTTCTCTCTT
66 AAGTCCCAATCTAAATCTCACCTAATATAATTCAACAAACACAAAATCAGGGTTTCTCTCTT
*
58562886 AGAAATCTTTGTTTCCTGCATTCAAACACATAAAATAAGACTGTTTCAATTGAACTAGAAATTTG
1 AGAAATCTTTGTTTCCTGCATTCAAACACATAAAATAGGACTGTTTCAATTGAACTAGAAATTTG
* *
58562951 AAGTCCCAATCTAAATCTCACCAAAAATAATTCAACAAACACAAAATCAGGGTTTCTCTCTT
66 AAGTCCCAATCTAAATCTCACCTAATATAATTCAACAAACACAAAATCAGGGTTTCTCTCTT
**
58563013 AGAAATCTTTGTTTCCTGCGGTCAAACACATAAAATAGGACTGTTTCAATTGAACTA-AAATTTG
1 AGAAATCTTTGTTTCCTGCATTCAAACACATAAAATAGGACTGTTTCAATTGAACTAGAAATTTG
58563077 AAGTCCCAATCTAAATCTCACCTAATATAATTCAACAAACACAAAATCAGGGTTTCTCTCT
66 AAGTCCCAATCTAAATCTCACCTAATATAATTCAACAAACACAAAATCAGGGTTTCTCTCT
58563138 AACTTCCACC
Statistics
Matches: 242, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
125 31 0.13
126 66 0.27
127 145 0.60
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (127 bp):
AGAAATCTTTGTTTCCTGCATTCAAACACATAAAATAGGACTGTTTCAATTGAACTAGAAATTTG
AAGTCCCAATCTAAATCTCACCTAATATAATTCAACAAACACAAAATCAGGGTTTCTCTCTT
Found at i:58564362 original size:13 final size:15
Alignment explanation
Indices: 58564344--58564380 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
58564334 AACTCGAGCA
58564344 TTAATTATTTAA-T-
1 TTAATTATTTAATTG
*
58564357 TTAATTAGTTAATTG
1 TTAATTATTTAATTG
58564372 TTAATTATT
1 TTAATTATT
58564381 ATTTGACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 11 0.55
14 1 0.05
15 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (15 bp):
TTAATTATTTAATTG
Found at i:58564556 original size:22 final size:20
Alignment explanation
Indices: 58564509--58564558 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
58564499 TGAAGTGAAG
**
58564509 GTGATATTGAATTATGAAAT
1 GTGATATTGAATTAAAAAAT
*
58564529 GCGATATTGAATTTAAAAAAAT
1 GTGATATTGAA-TT-AAAAAAT
58564551 GTGATATT
1 GTGATATT
58564559 ATGGACTTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 10 0.42
21 2 0.08
22 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (20 bp):
GTGATATTGAATTAAAAAAT
Found at i:58564923 original size:2 final size:2
Alignment explanation
Indices: 58564916--58564966 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
58564906 AATTTCATGA
58564916 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
58564958 AT AT AT AT A
1 AT AT AT AT A
58564967 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58574332 original size:13 final size:13
Alignment explanation
Indices: 58574312--58574350 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
58574302 AACGAAACAT
58574312 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
58574325 TA-AAAGAAAGAAA
1 -AGAAAGAAAGAAA
*
58574338 AGAAGGAAAGAAA
1 AGAAAGAAAGAAA
58574351 GGGAAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 1 0.04
13 21 0.91
14 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:58575076 original size:14 final size:15
Alignment explanation
Indices: 58575038--58575078 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
58575028 TTTGTGATTG
58575038 ATATGAATTTGATTGAA
1 ATATGAA-TTGA-TGAA
58575055 AT-TGAATTGA-GAA
1 ATATGAATTGATGAA
58575068 ATATGAATTGA
1 ATATGAATTGA
58575079 ATACCCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.22
14 8 0.35
15 4 0.17
16 4 0.17
17 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.37
Consensus pattern (15 bp):
ATATGAATTGATGAA
Found at i:58575368 original size:15 final size:16
Alignment explanation
Indices: 58575348--58575381 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
58575338 ATTGGCATTA
58575348 GAATTGAT-ATTGAAT
1 GAATTGATAATTGAAT
58575363 GAATTGATAAATTGAAT
1 GAATTGAT-AATTGAAT
58575380 GA
1 GA
58575382 TTTTATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (16 bp):
GAATTGATAATTGAAT
Found at i:58578819 original size:42 final size:42
Alignment explanation
Indices: 58578720--58578877 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 42
58578710 AGCTCGTACA
* * *
58578720 ATGCCAACGTCCCAGACGTAGTCTTACATGTAATCAAATAACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCATAT-ACG
58578763 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAATCATATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCATATACG
* * *
58578805 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATC-TCAAATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGT-AATCAT-ATA-CG
*
58578849 ATGCCAACATCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
58578878 AAAATCACAT
Statistics
Matches: 99, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
42 32 0.32
43 38 0.38
44 29 0.29
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCATATACG
Found at i:58578875 original size:86 final size:84
Alignment explanation
Indices: 58578720--58578877 Score: 196
Period size: 85 Copynumber: 1.8 Consensus size: 84
58578710 AGCTCGTACA
* * *
58578720 ATGCCAACGTCCCAGACGTAGTCTTACATGTAATCAAATAACGATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACATAGTCTTACACGTAATCAAAT-ACGATGCCACTATCCCAGACAGGGT
58578785 CTTACACGTAATCATATACG
65 CTTACACGTAATCATATACG
* *
58578805 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CGATGCCAAC-ATCCCAGAC-G
1 ATGCCAACGTCCCAGACATAGTCTTACACGT-AA--TCAAATACGATGCC-ACTATCCCAGACAG
58578867 TGGTCTTACAC
62 -GGTCTTACAC
58578878 AAAATCACAT
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
85 28 0.44
86 27 0.43
87 2 0.03
88 6 0.10
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATAGTCTTACACGTAATCAAATACGATGCCACTATCCCAGACAGGGTC
TTACACGTAATCATATACG
Found at i:58585199 original size:7 final size:8
Alignment explanation
Indices: 58585178--58585212 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
58585168 ACCAAATATT
58585178 TTAAAAAA
1 TTAAAAAA
58585186 TTAAAAAA
1 TTAAAAAA
58585194 TTAAAAAA
1 TTAAAAAA
58585202 TT-AAAAA
1 TTAAAAAA
58585209 TTAA
1 TTAA
58585213 TATTTTAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TTAAAAAA
Found at i:58587854 original size:14 final size:14
Alignment explanation
Indices: 58587837--58587864 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58587827 CCAAGTACTG
58587837 AAAACAAGATATAT
1 AAAACAAGATATAT
58587851 AAAACAAGATATAT
1 AAAACAAGATATAT
58587865 GATGCATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAACAAGATATAT
Found at i:58588631 original size:30 final size:30
Alignment explanation
Indices: 58588595--58588656 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
58588585 TCCTTAGATG
* *
58588595 ATTTTCATGTGCATTTCACATGAGCCATTA
1 ATTTTCATGTGCACTTCACATGAGCCACTA
*
58588625 ATTTTCATGTGCACTTCATATGAGCCACTA
1 ATTTTCATGTGCACTTCACATGAGCCACTA
58588655 AT
1 AT
58588657 AAACTCTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (30 bp):
ATTTTCATGTGCACTTCACATGAGCCACTA
Found at i:58590327 original size:30 final size:30
Alignment explanation
Indices: 58590291--58590352 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
58590281 ATAAGAGTTT
*
58590291 ATTAGTGGCTCACGTGAAGTACACATGAAA
1 ATTAGTGGCTCACGTGAAATACACATGAAA
* *
58590321 ATTAGTGGCTCATGTGAAATGCACATGAAA
1 ATTAGTGGCTCACGTGAAATACACATGAAA
58590351 AT
1 AT
58590353 CTTCTAAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (30 bp):
ATTAGTGGCTCACGTGAAATACACATGAAA
Found at i:58601290 original size:296 final size:293
Alignment explanation
Indices: 58600633--58601805 Score: 1039
Period size: 296 Copynumber: 3.9 Consensus size: 293
58600623 ACTCAATTAA
* * * * * * * *
58600633 TATATAGAAGTAATGGAGATAATAACTTGTGCATATTAAAATGAAAATTTATAAATTAGAATAAA
1 TATATACAACTAATAGAGATAATAACTTGTGCATATTAAAATAAAAATGTATAAAATATATTAAA
* * * * * *
58600698 ATGAAGCTTTGGTTGAATGGTAAAATT-AAGATTTTGCTAACTTAATTAGTGTGGGTTCAAA-CC
66 ATAAAGCTTTGGTTGAATGATAAATTTAAAG-TTTTACTAATTTAATTGGTGTGGGTTCAAATCC
* * * *
58600761 CTACTGTATGCATATTTTAATTTGTTTTTGTTAAAATAAAAAGATTAAAATAACTATTGTTAAAT
130 C-ACTATATGCATATTTTAATTTGTTTTTGTTAAAATAAAAAGACTAAAAT-AC----CTCAAAT
* * * * *
58600826 AGTATAACTTATTTTAATTACAAAAGGGTATTTTTGTAATTTTCTAACCGAGTTGGTGGCCCAAA
189 AGTATAACTTATTTTAATTA-AGAAGGGCATTTTTGTAATTTCCTAACTGAGTTGGT-GACC-AA
* * * * *
58600891 TGGGGGTGACATCAACTTAGTGAAACAATTAAT-AATTGTAAGG
251 TGAGGGTGACACCAACTTAGTAAAACACTTAATAAATAGTAA-G
* * * * *
58600934 ATAGATATACAACTACTGGAGATAATAACTTATGTATATTAAAATAAAAATGAATAAAATATATT
1 -T--ATATACAACTAATAGAGATAATAACTTGTGCATATTAAAATAAAAATGTATAAAATATATT
*
58600999 AAAATAAAGAC-TTGGTT-AAGTGATAAATTTAATA-TTTTACTAATTTAATTGGGGTGGGTTCA
63 AAAATAAAG-CTTTGGTTGAA-TGATAAATTTAA-AGTTTTACTAATTTAATTGGTGTGGGTTCA
* * *
58601061 AATCCCACTATATTCTTATTTTAATTTGTTTTTGTTAAAATGAAAAGACTAAAATGACCTCAAAT
125 AATCCCACTATATGCATATTTTAATTTGTTTTTGTTAAAATAAAAAGACTAAAAT-ACCTCAAAT
* * * *
58601126 AGTATAAATTATTTTAATTATGAAGGGCATTTTTGTAATTTCCTAACTGATTTGGTGACTCGATC
189 AGTATAACTTATTTTAATTAAGAAGGGCATTTTTGTAATTTCCTAACTGAGTTGGTGAC-CAAT-
* *
58601191 GAGGGTGACACCAACATAGTCAAACACTTAATAAATAGTAAG
252 GAGGGTGACACCAACTTAGTAAAACACTTAATAAATAGTAAG
* * *
58601233 TATATACAATTAGTAGAGATAA-AAATGTGTGCATATTAAAATAAAAATGTATAAAATATATTAA
1 TATATACAACTAATAGAGATAATAACT-TGTGCATATTAAAATAAAAATGTATAAAATATATTAA
** * * * ** *
58601297 AATAAAATTTTGGTTGAGTAATAAATTTAAAGTTTT-TTAGATCCAATTGGTGTGGGTTCAAATA
65 AATAAAGCTTTGGTTGAATGATAAATTTAAAGTTTTACTA-ATTTAATTGGTGTGGGTTCAAATC
* * *
58601361 TCA-TCATATGCATATTTTAATTTATTTTTGTTAAAATAAAAAGACTAAAATACCCTCAAACAGT
129 CCACT-ATATGCATATTTTAATTTGTTTTTGTTAAAATAAAAAGACTAAAATA-CCTCAAATAGT
* *** * *
58601425 ATAACTTATTTTAATTACGAAATAACATTTTTATAATTTCCTAA-TCGAGTTGGTGACCTAGTTG
192 ATAACTTATTTTAATTAAG-AAGGGCATTTTTGTAATTTCCTAACT-GAGTTGGTGACC-A-ATG
* *
58601489 AGGATGACACCAACTTAGTAAAATACTTAATAAATAGTATA-
253 AGGGTGACACCAACTTAGTAAAACACTTAATAAATAGTA-AG
* * ** *
58601530 TTTATACAACTAATTGAGATAATAACTTGTGCATATT-AAA-AAACGTGATTATCAAATATATTA
1 TATATACAACTAATAGAGATAATAACTTGTGCATATTAAAATAAAAATG--TATAAAATATATTA
** * * ** **
58601593 AAACGAAGCTTTGGTTGAATGGTAAATTTAAAGTTTTATTAATTTAATTGGCATGTATTCAAATC
64 AAATAAAGCTTTGGTTGAATGATAAATTTAAAGTTTTACTAATTTAATTGGTGTGGGTTCAAATC
** * * ** *
58601658 TTA-TCATATG--TATTTTAGTTGGTTTTTGTTAAAATAAAAA-TTTAAAATACCCTCAAATGGT
129 CCACT-ATATGCATATTTTAATTTGTTTTTGTTAAAATAAAAAGACTAAAATA-CCTCAAATAGT
* **** * **
58601719 ACAACTTATTTTAATTACAGAAAAATATTCTCATAATTTCCTAACTGAGTTGGTGACCCAATTGA
192 ATAACTTATTTTAATTA-AGAAGGGCATTTTTGTAATTTCCTAACTGAGTTGGTGA-CCAA-TGA
* * *
58601784 AGGTGACACAAACTCAGTAAAA
254 GGGTGACACCAACTTAGTAAAA
58601806 TTCAAAAAGA
Statistics
Matches: 724, Mismatches: 117, Indels: 68
0.80 0.13 0.07
Matches are distributed among these distances:
294 85 0.12
295 44 0.06
296 175 0.24
297 164 0.23
298 13 0.02
299 59 0.08
300 31 0.04
302 1 0.00
303 2 0.00
304 144 0.20
305 5 0.01
306 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (293 bp):
TATATACAACTAATAGAGATAATAACTTGTGCATATTAAAATAAAAATGTATAAAATATATTAAA
ATAAAGCTTTGGTTGAATGATAAATTTAAAGTTTTACTAATTTAATTGGTGTGGGTTCAAATCCC
ACTATATGCATATTTTAATTTGTTTTTGTTAAAATAAAAAGACTAAAATACCTCAAATAGTATAA
CTTATTTTAATTAAGAAGGGCATTTTTGTAATTTCCTAACTGAGTTGGTGACCAATGAGGGTGAC
ACCAACTTAGTAAAACACTTAATAAATAGTAAG
Found at i:58614236 original size:6 final size:6
Alignment explanation
Indices: 58614225--58614262 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
58614215 CCGCCTCATT
58614225 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CC
58614263 CCTTAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTCTC
Found at i:58618195 original size:48 final size:47
Alignment explanation
Indices: 58618121--58618274 Score: 128
Period size: 44 Copynumber: 3.4 Consensus size: 47
58618111 ATCCTATACT
58618121 CCTGAAGTTGCAGTGG-G-ATGGATTGAAGATCATAGCAAACTTTATCTC
1 CCTGAAGTTGCAGTGGAGCA-GG-TTGAAGAT-ATAGCAAACTTTATCTC
*
58618169 CCTGAAGTTGCAGTGGAGCAGGTTGAAG-T-TA-C-AAGTCTTATCTC
1 CCTGAAGTTGCAGTGGAGCAGGTTGAAGATATAGCAAACT-TTATCTC
* * *** * *
58618213 CCTAAAGCTGCAGTGGAGCAAACTGAAGATA-ATG-AATC-TTATTTC
1 CCTGAAGTTGCAGTGGAGCAGGTTGAAGATATA-GCAAACTTTATCTC
58618258 CCTGAAGTTGCAGTGGA
1 CCTGAAGTTGCAGTGGA
58618275 ACAGATTAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
43 3 0.03
44 31 0.36
45 25 0.29
47 2 0.02
48 22 0.25
49 3 0.03
50 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (47 bp):
CCTGAAGTTGCAGTGGAGCAGGTTGAAGATATAGCAAACTTTATCTC
Found at i:58618270 original size:45 final size:44
Alignment explanation
Indices: 58618162--58618274 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 44
58618152 ATAGCAAACT
*** * *
58618162 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATACAAATC
* *
58618206 TTATCTCCCTAAAGCTGCAGTGGAGCAAACTGAAGATA-ATGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATACA--AATC
*
58618251 TTATTTCCCTGAAGTTGCAGTGGA
1 TTATCTCCCTGAAGTTGCAGTGGA
58618275 ACAGATTAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
43 1 0.02
44 32 0.56
45 24 0.42
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATACAAATC
Found at i:58618458 original size:180 final size:181
Alignment explanation
Indices: 58618147--58618541 Score: 558
Period size: 180 Copynumber: 2.2 Consensus size: 181
58618137 GATGGATTGA
* * * *
58618147 AGATCATAGCAAACTTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCT
1 AGATCATAGCAAACTTTATCTCCCTGAAGTTGTAGCGAAGCAGGTTGAAGTTACAAGTCTTAACT
* * **
58618212 CCCTAAAGCTGCAGTGGAGCAAACTGAAGATAATGAATCTTATTTCCCTGAAGTTGCAGTGGAAC
66 CCCTAAAGCTGCAGTAGAGCAAACTGAAGATAACGAATCTTATTTCCCAAAAGTTGCAGTGGAAC
* * * *
58618277 AGATTAAAGTTATAAATTACAGATTTTATCTCTCTAAAGTTACAGTAGGGC
131 AGATTAAAGCTATAAATTAAAGATCTTATCTCTCTAAAGTTACAGTAGAGC
* *
58618328 AG-TCATATCAAACTTTATCTCCCTGAAGTTGTAGCGAAGCAGGTTGAAGTTATAAGTCTTAACT
1 AGATCATAGCAAACTTTATCTCCCTGAAGTTGTAGCGAAGCAGGTTGAAGTTACAAGTCTTAACT
* * * * *
58618392 CCCTGAAGTTGTAGTAGAGCAGACTGAAGATAGCGAATCTTATTTCCCAAAAGTTGCAGTGGAAC
66 CCCTAAAGCTGCAGTAGAGCAAACTGAAGATAACGAATCTTATTTCCCAAAAGTTGCAGTGGAAC
* * **
58618457 AGATTAAAGCTATAAATTAAATATCTTATCTTTCTAAAGTTGTAGTAGAGC
131 AGATTAAAGCTATAAATTAAAGATCTTATCTCTCTAAAGTTACAGTAGAGC
* *
58618508 AGATCATAGCAAACCTTATCTCCCTTAAGTTGTA
1 AGATCATAGCAAACTTTATCTCCCTGAAGTTGTA
58618542 CTGGAATAGT
Statistics
Matches: 187, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
180 157 0.84
181 30 0.16
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (181 bp):
AGATCATAGCAAACTTTATCTCCCTGAAGTTGTAGCGAAGCAGGTTGAAGTTACAAGTCTTAACT
CCCTAAAGCTGCAGTAGAGCAAACTGAAGATAACGAATCTTATTTCCCAAAAGTTGCAGTGGAAC
AGATTAAAGCTATAAATTAAAGATCTTATCTCTCTAAAGTTACAGTAGAGC
Found at i:58620457 original size:26 final size:25
Alignment explanation
Indices: 58620424--58620821 Score: 218
Period size: 26 Copynumber: 15.8 Consensus size: 25
58620414 TCTTATTTAT
58620424 TTATTTATTTTAAATCTTTTCATATA
1 TTATTTATTTTAAATCTTTT-ATATA
* *
58620450 TTACTTATTTTAAACTGTTTTAT-TA
1 TTATTTATTTTAAA-TCTTTTATATA
* * * *
58620475 TTACTTATTTTAAGTTTTATTTTCATGTA
1 TTATTTATTTTAA---ATCTTTT-ATATA
*
58620504 TTA-TTATTTTAAA-C--TTATACA
1 TTATTTATTTTAAATCTTTTATATA
* *
58620525 TTATTCATTTTAAATTGTTTTATATA
1 TTATTTATTTTAAA-TCTTTTATATA
* * *
58620551 GTATTCATTTCAAA-CTGTTT-TAT-
1 TTATTTATTTTAAATCT-TTTATATA
*
58620574 TGTATACTATTTTAAA-CTATTATATATA
1 T-TAT-TTATTTTAAATCT-TT-TATATA
58620602 TTATTTATTTTAAAT-TGCTTTATATA
1 TTATTTATTTTAAATCT--TTTATATA
* *
58620628 TTATTTATTTTAAACTGTTTTATATT
1 TTATTTATTTTAAA-TCTTTTATATA
* *
58620654 TTATTTATCTTAAAT-TTTTTTCATA
1 TTATTTATTTTAAATCTTTTAT-ATA
** * * * *
58620679 TGGTTTATTTTGAACCAATTTGTATA
1 TTATTTATTTTAAATC-TTTTATATA
*
58620705 TTATTTATTTTAAATTTTTTCATATA
1 TTATTTATTTTAAATCTTTT-ATATA
*
58620731 TTA-TT-TTTTAAA-ATTTT-TATA
1 TTATTTATTTTAAATCTTTTATATA
* *
58620752 TTATTTACTTTAAAT-TGTTTCATTTA
1 TTATTTATTTTAAATCT-TTT-ATATA
* *
58620778 TCATTTATTTTAAACCTTTT-TATA
1 TTATTTATTTTAAATCTTTTATATA
* *
58620802 TTATTTACTTTAAATTTTTT
1 TTATTTATTTTAAATCTTTT
58620822 TTACATATTA
Statistics
Matches: 290, Mismatches: 50, Indels: 66
0.71 0.12 0.16
Matches are distributed among these distances:
21 13 0.04
22 13 0.04
23 11 0.04
24 41 0.14
25 47 0.16
26 123 0.42
27 24 0.08
28 13 0.04
29 5 0.02
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.60
Consensus pattern (25 bp):
TTATTTATTTTAAATCTTTTATATA
Found at i:58620686 original size:77 final size:75
Alignment explanation
Indices: 58620524--58620822 Score: 231
Period size: 77 Copynumber: 4.0 Consensus size: 75
58620514 AAACTTATAC
* * * * * * *
58620524 ATTATTCATTTTAAATTGTTTTATATAGTATTCATTTCAAACTG-TTT-TATTGTATACTATTTT
1 ATTATTTATTTTAAATTG-TTTATATATTATTTATTTTAAACTGTTTTATATTTTAT-TTATCTT
* *
58620587 AAACTATTATATAT
64 AAA-T-TTTTTTAT
58620601 ATTATTTATTTTAAATTGCTTTATATATTATTTATTTTAAACTGTTTTATATTTTATTTATCTTA
1 ATTATTTATTTTAAATTG-TTTATATATTATTTATTTTAAACTGTTTTATATTTTATTTATCTTA
58620666 AATTTTTTTCAT
65 AATTTTTTT-AT
** **** * * *
58620678 ATGGTTTATTTTGAACCAATTTGTATATTATTTATTTTAAA-TTTTTTCATATATTATTT-T-TT
1 ATTATTTATTTT-AAATTGTTTATATATTATTTATTTTAAACTGTTTT-ATATTTTATTTATCTT
*
58620740 AAA-ATTTTTAT
64 AAATTTTTTTAT
* * *
58620751 ATTATTTACTTTAAATTGTTTCATTTATCATTTATTTTAAACCT-TTTTATA--TTATTTA-CTT
1 ATTATTTATTTTAAATTGTTT-ATATATTATTTATTTTAAA-CTGTTTTATATTTTATTTATC-T
58620812 TAAATTTTTTT
63 TAAATTTTTTT
58620823 TACATATTAT
Statistics
Matches: 179, Mismatches: 31, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
71 6 0.03
72 5 0.03
73 35 0.20
74 14 0.08
75 6 0.03
76 10 0.06
77 83 0.46
78 13 0.07
79 7 0.04
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (75 bp):
ATTATTTATTTTAAATTGTTTATATATTATTTATTTTAAACTGTTTTATATTTTATTTATCTTAA
ATTTTTTTAT
Found at i:58620738 original size:23 final size:23
Alignment explanation
Indices: 58620712--58620783 Score: 58
Period size: 24 Copynumber: 3.1 Consensus size: 23
58620702 ATATTATTTA
58620712 TTTTAAATTTTTTCATATATTATT
1 TTTTAAATTTTTTCATATATTA-T
*
58620736 TTTTAAAATTTTT-ATATTATT-T
1 TTTTAAATTTTTTCATA-TATTAT
* * * *
58620758 ACTTTAAATTGTTTCATTTATCAT
1 -TTTTAAATTTTTTCATATATTAT
58620782 TT
1 TT
58620784 ATTTTAAACC
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 1 0.03
23 17 0.46
24 19 0.51
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (23 bp):
TTTTAAATTTTTTCATATATTAT
Found at i:58622231 original size:2 final size:2
Alignment explanation
Indices: 58622226--58622255 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
58622216 ATATATATAT
*
58622226 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
58622256 GTTGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:58634474 original size:12 final size:12
Alignment explanation
Indices: 58634459--58634490 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
58634449 TAATGAAAAT
58634459 ATAAATAAAGAA
1 ATAAATAAAGAA
58634471 ATAAATAAAGAA
1 ATAAATAAAGAA
*
58634483 ATGAATAA
1 ATAAATAA
58634491 GGCTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (12 bp):
ATAAATAAAGAA
Found at i:58634856 original size:3 final size:3
Alignment explanation
Indices: 58634842--58634912 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
58634832 CAAATAAAAC
*
58634842 TAA TAA TGA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
58634888 TAA TAA -AA CTAA T-T TAA TAA TAA TA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TA
58634913 GAAATAACAA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 3 0.05
3 52 0.87
4 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:58636669 original size:5 final size:5
Alignment explanation
Indices: 58636650--58636686 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
58636640 AGTTTTGCAT
*
58636650 TATTA T-TTT TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
58636687 ATTTATTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 26 0.90
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TATTA
Found at i:58639771 original size:45 final size:43
Alignment explanation
Indices: 58639707--58640008 Score: 326
Period size: 45 Copynumber: 7.0 Consensus size: 43
58639697 TTAGAACGAA
*
58639707 TATCCATT-AATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGGG
1 TATCC-TTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACC--G
* * *
58639752 TATCCATGAATATAAAGGTGGTTGCTAAATGTTGATTCCACTGG
1 TATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCAC-CG
* *
58639796 ATATCCATGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACCG
1 -TATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACCG
* * * * * *
58639840 TATCTTTGATTATAAAAGG-GGCTGCTATGTGCTGATTCC-CCA
1 TATCCTTGAATAT-AAAGGTGGTTGCTAAGTGTTGATTCCACCG
58639882 TATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACCG
1 TATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACCG
* * * * *
58639925 TATCTTTGATTATGAAAGG-GGTTGCTATGTGCTAATTCC-CCG
1 TATCCTTGAATAT-AAAGGTGGTTGCTAAGTGTTGATTCCACCG
* * *
58639967 TATCCTTGATTATAAAGGTGTTTGCTATGTGTTGATTCCACC
1 TATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACC
58640009 AGATATCATT
Statistics
Matches: 218, Mismatches: 30, Indels: 20
0.81 0.11 0.07
Matches are distributed among these distances:
41 10 0.05
42 62 0.28
43 58 0.27
44 13 0.06
45 75 0.34
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (43 bp):
TATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACCG
Found at i:58639876 original size:43 final size:42
Alignment explanation
Indices: 58639717--58640053 Score: 284
Period size: 45 Copynumber: 7.8 Consensus size: 42
58639707 TATCCATTAA
* * *
58639717 TATAAAGGTGGTTGCTAAGTGCTGATTCCACCGGGTATCCATGAA
1 TATAAAGGTGGTTGCTATGTGCTGATT-CACC--GTATCCTTGAT
** * * * *
58639762 TATAAAGGTGGTTGCTAAATGTTGATTCCACTGGATATCCATGAA
1 TATAAAGGTGGTTGCTATGTGCTGATT-CAC-CG-TATCCTTGAT
* * *
58639807 TATAAAGGTGGTTGCTAAGTGTTGATTCGACCGTATCTTTGAT
1 TATAAAGGTGGTTGCTATGTGCTGATTC-ACCGTATCCTTGAT
* * * *
58639850 TATAAAAGG-GGCTGCTATGTGCTGATTCCCCATATCCTTGAA
1 TAT-AAAGGTGGTTGCTATGTGCTGATTCACCGTATCCTTGAT
* * *
58639892 TATAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCTTTGAT
1 TATAAAGGTGGTTGCTATGTGCTGATT-CACCGTATCCTTGAT
* *
58639935 TATGAAAGG-GGTTGCTATGTGCTAATTCCCCGTATCCTTGAT
1 TAT-AAAGGTGGTTGCTATGTGCTGATTCACCGTATCCTTGAT
* * * *
58639977 TATAAAGGTGTTTGCTATGTGTTGATTCCACCAGATATCATTGTT
1 TATAAAGGTGGTTGCTATGTGCTGATT-CACC-G-TATCCTTGAT
* * *
58640022 TATAAGGGTGG-TGCTATGTGCTCATCCACCGT
1 TATAAAGGTGGTTGCTATGTGCTGATTCACCGT
58640054 GTATCTGTTA
Statistics
Matches: 243, Mismatches: 38, Indels: 26
0.79 0.12 0.08
Matches are distributed among these distances:
41 11 0.05
42 60 0.25
43 62 0.26
44 26 0.11
45 84 0.35
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (42 bp):
TATAAAGGTGGTTGCTATGTGCTGATTCACCGTATCCTTGAT
Found at i:58639910 original size:85 final size:86
Alignment explanation
Indices: 58639706--58640043 Score: 373
Period size: 85 Copynumber: 3.9 Consensus size: 86
58639696 ATTAGAACGA
* ** *
58639706 ATATCCATT-AATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGGGTATCCATGAATAT-AAAG
1 ATATCC-TTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACC-GGTATCTTTGATTATAAAAG
** * *
58639769 GTGGTTGCTAAATGTTGATTCCACTGG
64 G-GGTTGCTATGTGCTGATTCC-C--C
* *
58639796 ATATCCATGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACC-GTATCTTTGATTATAAAAGGG
1 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACCGGTATCTTTGATTATAAAAGGG
*
58639860 GCTGCTATGTGCTGATTCCCC
66 GTTGCTATGTGCTGATTCCCC
*
58639881 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACC-GTATCTTTGATTATGAAAGGG
1 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACCGGTATCTTTGATTATAAAAGGG
*
58639945 GTTGCTATGTGCTAATTCCCC
66 GTTGCTATGTGCTGATTCCCC
* * * * * * *
58639966 GTATCCTTGATTATAAAGGTGTTTGCTATGTGTTGATTCCACCAGATATCATTG-TT-TATAAGG
1 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACC-GGTATCTTTGATTATAAAAGG
*
58640029 GTGGTGCTATGTGCT
65 G-GTTGCTATGTGCT
58640044 CATCCACCGT
Statistics
Matches: 218, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
85 125 0.57
86 14 0.06
87 8 0.04
88 27 0.12
89 6 0.03
90 38 0.17
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (86 bp):
ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACCGGTATCTTTGATTATAAAAGGG
GTTGCTATGTGCTGATTCCCC
Found at i:58640015 original size:130 final size:132
Alignment explanation
Indices: 58639717--58640037 Score: 370
Period size: 130 Copynumber: 2.5 Consensus size: 132
58639707 TATCCATTAA
* * *
58639717 TATAAAGGTGGTTGCTAAGTGCTGATTCCACCGGGTATCCATGAATATAAAGGTGGTTGCTAAAT
1 TATAAAGGTGGTTGCTATGTGCTGATTCCACC-GATATCCTTGAATATAAAGGTGGTTGCTAAAT
* * * *
58639782 GTTGATTCCACTGGATATCCATGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACCGTATCTTT
65 GTTGATTCCACTCGATATCCATGAATATAAAGGTGGTTGCTAAGTGCTAATTCGACCGTATCCTT
58639847 GAT
130 GAT
* *
58639850 TATAAAAGG-GGCTGCTATGTGCTGATTCC-CC-ATATCCTTGAATATAAAGGTGGTTGCTAAGT
1 TAT-AAAGGTGGTTGCTATGTGCTGATTCCACCGATATCCTTGAATATAAAGGTGGTTGCTAAAT
** * * *
58639912 GTTGATTCCAC-CG-TATCTTTGATTATGAAAGG-GGTTGCTATGTGCTAATTC-CCCGTATCCT
65 GTTGATTCCACTCGATATCCATGAATAT-AAAGGTGGTTGCTAAGTGCTAATTCGACCGTATCCT
58639973 TGAT
129 TGAT
* * * ** *
58639977 TATAAAGGTGTTTGCTATGTGTTGATTCCACCAGATATCATTGTTTATAAGGGTGG-TGCTA
1 TATAAAGGTGGTTGCTATGTGCTGATTCCACC-GATATCCTTGAATATAAAGGTGGTTGCTA
58640038 TGTGCTCATC
Statistics
Matches: 161, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
126 5 0.03
127 32 0.20
128 28 0.17
129 11 0.07
130 57 0.35
132 2 0.01
133 21 0.13
134 5 0.03
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (132 bp):
TATAAAGGTGGTTGCTATGTGCTGATTCCACCGATATCCTTGAATATAAAGGTGGTTGCTAAATG
TTGATTCCACTCGATATCCATGAATATAAAGGTGGTTGCTAAGTGCTAATTCGACCGTATCCTTG
AT
Found at i:58642867 original size:36 final size:36
Alignment explanation
Indices: 58642827--58642898 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
58642817 ACCCTCACTT
*
58642827 TTAATCGGTCCCTAAACTTCAAACTATTCTATTTAC
1 TTAATCGGTCCCTAAACTTCAAACTATTCTAATTAC
58642863 TTAATCGGTCCCTAAACTTCAAACTATTCTAATTAC
1 TTAATCGGTCCCTAAACTTCAAACTATTCTAATTAC
58642899 ATCTTTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (36 bp):
TTAATCGGTCCCTAAACTTCAAACTATTCTAATTAC
Found at i:58644612 original size:2 final size:2
Alignment explanation
Indices: 58644605--58644632 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58644595 CTATGACAAC
58644605 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
58644633 GTAATGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58647221 original size:22 final size:22
Alignment explanation
Indices: 58647196--58647238 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
58647186 AGCATCAATC
58647196 CTAATAAAAATTAACATCAGTA
1 CTAATAAAAATTAACATCAGTA
* *
58647218 CTAATGAAAATTAGCATCAGT
1 CTAATAAAAATTAACATCAGT
58647239 CTATTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (22 bp):
CTAATAAAAATTAACATCAGTA
Found at i:58650421 original size:39 final size:38
Alignment explanation
Indices: 58650373--58650447 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 38
58650363 AATTTAAAAA
*
58650373 GTATATTTAATGCAATAAAATATTTATTATATTTATTT
1 GTATATTTAATACAATAAAATATTTATTATATTTATTT
*
58650411 GTATATTTTAATATAATAAAATATTTATTATATTTAT
1 GTATA-TTTAATACAATAAAATATTTATTATATTTAT
58650448 GATAGTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 5 0.15
39 29 0.85
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (38 bp):
GTATATTTAATACAATAAAATATTTATTATATTTATTT
Found at i:58650457 original size:39 final size:39
Alignment explanation
Indices: 58650372--58650467 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 39
58650362 AAATTTAAAA
**
58650372 AGTATATTTAATGCAATAAAATATTTATTATATTTATTTGT
1 AGTAT-TTTAATATAATAAAATATTTATTATATTTA-TTGT
58650413 A-TATTTTAATATAATAAAATATTTATTATATTTA-TGAT
1 AGTATTTTAATATAATAAAATATTTATTATATTTATTG-T
58650451 AGTATTTTTTAATATAA
1 AGTA--TTTTAATATAA
58650468 ATACTTTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
37 2 0.04
38 2 0.04
39 30 0.61
40 3 0.06
41 12 0.24
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (39 bp):
AGTATTTTAATATAATAAAATATTTATTATATTTATTGT
Found at i:58659820 original size:29 final size:30
Alignment explanation
Indices: 58659761--58659818 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
58659751 TCCGAGCCTT
*
58659761 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
58659791 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
58659819 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:58660049 original size:13 final size:13
Alignment explanation
Indices: 58660031--58660061 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58660021 TTCCAGCAAC
58660031 TATGAATTTATTT
1 TATGAATTTATTT
58660044 TATGAATTTATTT
1 TATGAATTTATTT
*
58660057 GATGA
1 TATGA
58660062 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:58665631 original size:50 final size:50
Alignment explanation
Indices: 58665556--58665798 Score: 405
Period size: 50 Copynumber: 4.8 Consensus size: 50
58665546 ATTTGGGTAA
58665556 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
58665606 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
58665656 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
58665706 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
58665756 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
58665799 TGTTATTATC
Statistics
Matches: 180, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 146 0.81
51 34 0.19
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:58668774 original size:109 final size:108
Alignment explanation
Indices: 58668583--58668825 Score: 443
Period size: 109 Copynumber: 2.2 Consensus size: 108
58668573 AGTGATTACA
*
58668583 CAAAACATTGTCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAAT
1 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAAT
*
58668648 CGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAACG
66 CGACACCCAGCACCTTAGGGCATGTTTTCTCG-ATTTCCAAACG
58668692 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAAT
1 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAAT
58668757 CGACACCCAGCACCTTAGGGCATGTTTTCTCGATTTCCAAACG
66 CGACACCCAGCACCTTAGGGCATGTTTTCTCGATTTCCAAACG
*
58668800 CAAAACATTGCCTTA-TTTGAAATTTT
1 CAAAACATTGCCTTATTTTAAAATTTT
58668826 ANNNNNNNNN
Statistics
Matches: 131, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
107 10 0.08
108 25 0.19
109 96 0.73
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (108 bp):
CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAAT
CGACACCCAGCACCTTAGGGCATGTTTTCTCGATTTCCAAACG
Found at i:58672847 original size:2 final size:2
Alignment explanation
Indices: 58672840--58672909 Score: 63
Period size: 2 Copynumber: 35.5 Consensus size: 2
58672830 AAGTATTTAC
* * * ** *
58672840 AT AT AT AT AT AT AT GT AT AT AG AT -T AT A- AA AT GC AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58672880 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
58672910 AGTATGTATG
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
1 2 0.04
2 51 0.93
3 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:58673072 original size:12 final size:14
Alignment explanation
Indices: 58673047--58673079 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
58673037 AGGAAAAAGA
58673047 GTATATAGATATAT
1 GTATATAGATATAT
58673061 GTATATA-A-ATAT
1 GTATATAGATATAT
58673073 GTATATA
1 GTATATA
58673080 TAAAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 1 0.05
14 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (14 bp):
GTATATAGATATAT
Found at i:58673080 original size:14 final size:14
Alignment explanation
Indices: 58673048--58673130 Score: 61
Period size: 14 Copynumber: 6.1 Consensus size: 14
58673038 GGAAAAAGAG
* *
58673048 TATATAGATATATG
1 TATATAAATATATA
*
58673062 TATATAAATATGTA
1 TATATAAATATATA
58673076 TATATAAA-A-AGTA
1 TATATAAATATA-TA
58673089 T-T-T-AATATATA
1 TATATAAATATATA
*
58673100 TAT-TAAATAAATTA
1 TATATAAATATA-TA
58673114 TATATGAAATATATA
1 TATAT-AAATATATA
58673129 TA
1 TA
58673131 AGCACTTATG
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
10 2 0.04
11 5 0.09
12 4 0.07
13 9 0.16
14 24 0.44
15 5 0.09
16 6 0.11
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
TATATAAATATATA
Found at i:58673229 original size:3 final size:3
Alignment explanation
Indices: 58673211--58673300 Score: 51
Period size: 3 Copynumber: 30.7 Consensus size: 3
58673201 AAATAGAAAT
* * * * * * *
58673211 ATA ATG ATA GTA ATA ATA ACA TTA ATA TTA ATA ATA ATA GTA A-A GATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * *
58673259 ATA AT- ATA ATA A-A AAA ATA AAA AAA ATA ATA GTA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
58673301 GTCAACTTTA
Statistics
Matches: 64, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
2 5 0.08
3 59 0.92
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:58676213 original size:13 final size:13
Alignment explanation
Indices: 58676197--58676239 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
58676187 AATAAACAGA
*
58676197 TAATAGAAACAAT
1 TAATAGAATCAAT
58676210 TAATCA-AATCAAT
1 TAAT-AGAATCAAT
58676223 TAATAGAATCAAT
1 TAATAGAATCAAT
58676236 TAAT
1 TAAT
58676240 GCAATCAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 1 0.04
13 25 0.93
14 1 0.04
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (13 bp):
TAATAGAATCAAT
Found at i:58676245 original size:13 final size:13
Alignment explanation
Indices: 58676206--58676246 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
58676196 ATAATAGAAA
58676206 CAATTAAT-CAAAT
1 CAATTAATGC-AAT
58676219 CAATTAATAG-AAT
1 CAATTAAT-GCAAT
58676232 CAATTAATGCAAT
1 CAATTAATGCAAT
58676245 CA
1 CA
58676247 GCTATCCGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 24 0.96
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (13 bp):
CAATTAATGCAAT
Found at i:58679213 original size:30 final size:30
Alignment explanation
Indices: 58679145--58679218 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 30
58679135 TGCGAACCCA
* *
58679145 GTGTCCAATGTAAATAAATATTATTTGAAG
1 GTGTCCAATGTAAATAAATAATATTTCAAG
58679175 GTGT----TGTAAATAAATAATATTTCAAG
1 GTGTCCAATGTAAATAAATAATATTTCAAG
58679201 GTGTCCAATGTAAATAAA
1 GTGTCCAATGTAAATAAA
58679219 AAAAAACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 24 0.63
30 14 0.37
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (30 bp):
GTGTCCAATGTAAATAAATAATATTTCAAG
Found at i:58680228 original size:17 final size:19
Alignment explanation
Indices: 58680206--58680240 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58680196 TTTATTATCG
58680206 TTTATTT-C-ATACTTTTT
1 TTTATTTCCAATACTTTTT
58680223 TTTATTTCCAATACTTTT
1 TTTATTTCCAATACTTTT
58680241 AACATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATTTCCAATACTTTTT
Found at i:58686345 original size:9 final size:9
Alignment explanation
Indices: 58686331--58686361 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
58686321 GTTAAACGAA
58686331 TCGAGTTAT
1 TCGAGTTAT
*
58686340 TCGAGTTAA
1 TCGAGTTAT
58686349 TCGAGTTAT
1 TCGAGTTAT
58686358 TCGA
1 TCGA
58686362 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:58686439 original size:9 final size:9
Alignment explanation
Indices: 58686415--58686451 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
58686405 TGAGTTTTCG
*
58686415 AATTCAAAT
1 AATTCGAAT
*
58686424 AACTCGAAT
1 AATTCGAAT
58686433 AATTCGAAT
1 AATTCGAAT
58686442 AATTCGAAT
1 AATTCGAAT
58686451 A
1 A
58686452 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:58687259 original size:5 final size:5
Alignment explanation
Indices: 58687249--58687275 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
58687239 CTCGAAAATT
58687249 TTCGA TTCGA TTCGA TTCGA TTCGA TT
1 TTCGA TTCGA TTCGA TTCGA TTCGA TT
58687276 TGATCGAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTCGA
Found at i:58688999 original size:45 final size:45
Alignment explanation
Indices: 58688935--58689025 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
58688925 TTAGAGAAGT
* *
58688935 TGGATTTCTTGATCATGTGATTTCAATAGAAGGCATGCGGGTTGA
1 TGGATTTCTTGATCATGTGATTTCAACAGAAGGCATACGGGTTGA
58688980 TGGATTTCTTGATCATGTGATTTCAACAGAAGGCATACGGGTTGA
1 TGGATTTCTTGATCATGTGATTTCAACAGAAGGCATACGGGTTGA
58689025 T
1 T
58689026 CCGAGCAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (45 bp):
TGGATTTCTTGATCATGTGATTTCAACAGAAGGCATACGGGTTGA
Found at i:58691893 original size:3 final size:3
Alignment explanation
Indices: 58691885--58691986 Score: 177
Period size: 3 Copynumber: 33.3 Consensus size: 3
58691875 CCTTTTTAGC
58691885 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
*
58691931 CTT CATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
58691977 ATT ATT ATT A
1 ATT ATT ATT A
58691987 CTATACTAGT
Statistics
Matches: 95, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
3 91 0.96
4 4 0.04
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:58692244 original size:2 final size:2
Alignment explanation
Indices: 58692237--58692272 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
58692227 GTCTATATCC
*
58692237 AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58692273 ATCTACATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:58692345 original size:22 final size:20
Alignment explanation
Indices: 58692308--58692349 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
58692298 TTTATATTTT
58692308 TATATCTTATAATTTATGTA
1 TATATCTTATAATTTATGTA
*
58692328 TATATTTTAATAATTTTATGTA
1 TATATCTT-ATAA-TTTATGTA
58692350 CATACATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (20 bp):
TATATCTTATAATTTATGTA
Found at i:58695531 original size:26 final size:27
Alignment explanation
Indices: 58695476--58695524 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
58695466 ATAAAATACA
*
58695476 TCTTTGCATTCCTTTTTGAGCTAATAT
1 TCTTTGCATTCCTTTTTGAGATAATAT
58695503 TCTTT-CATT-CTTTTTGA-ATAAT
1 TCTTTGCATTCCTTTTTGAGATAAT
58695525 TATTTCTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 8 0.38
26 4 0.19
27 5 0.24
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.55
Consensus pattern (27 bp):
TCTTTGCATTCCTTTTTGAGATAATAT
Found at i:58708599 original size:116 final size:116
Alignment explanation
Indices: 58708395--58708626 Score: 464
Period size: 116 Copynumber: 2.0 Consensus size: 116
58708385 CTTGACCACT
58708395 CTTATCTGATTCTGGCGAATTACCACATTATTTCTGACAGCCTTGACTGCACATTTCTATACAGT
1 CTTATCTGATTCTGGCGAATTACCACATTATTTCTGACAGCCTTGACTGCACATTTCTATACAGT
58708460 GACATATGATCACTTATTTGGCGTGTAGGGTTGGATAGGTACTTATTACCC
66 GACATATGATCACTTATTTGGCGTGTAGGGTTGGATAGGTACTTATTACCC
58708511 CTTATCTGATTCTGGCGAATTACCACATTATTTCTGACAGCCTTGACTGCACATTTCTATACAGT
1 CTTATCTGATTCTGGCGAATTACCACATTATTTCTGACAGCCTTGACTGCACATTTCTATACAGT
58708576 GACATATGATCACTTATTTGGCGTGTAGGGTTGGATAGGTACTTATTACCC
66 GACATATGATCACTTATTTGGCGTGTAGGGTTGGATAGGTACTTATTACCC
58708627 TAAATGATGT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (116 bp):
CTTATCTGATTCTGGCGAATTACCACATTATTTCTGACAGCCTTGACTGCACATTTCTATACAGT
GACATATGATCACTTATTTGGCGTGTAGGGTTGGATAGGTACTTATTACCC
Found at i:58714917 original size:20 final size:19
Alignment explanation
Indices: 58714892--58714939 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
58714882 GAATTTTTTG
58714892 GGTAATTTTCAGGTAATTC
1 GGTAATTTTCAGGTAATTC
**
58714911 AGGTAATTTTTGGGTAATTC
1 -GGTAATTTTCAGGTAATTC
58714931 GGTTAATTT
1 GG-TAATTT
58714940 GGTTAATTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (19 bp):
GGTAATTTTCAGGTAATTC
Found at i:58714937 original size:9 final size:9
Alignment explanation
Indices: 58714925--58714973 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
58714915 AATTTTTGGG
58714925 TAATTCGGT
1 TAATTCGGT
*
58714934 TAATTTGGT
1 TAATTCGGT
58714943 TAATTCGGT
1 TAATTCGGT
*
58714952 TAA-TCGGG
1 TAATTCGGT
*
58714960 TAATTCGGG
1 TAATTCGGT
58714969 TAATT
1 TAATT
58714974 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
8 7 0.19
9 29 0.81
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.43
Consensus pattern (9 bp):
TAATTCGGT
Found at i:58714946 original size:18 final size:18
Alignment explanation
Indices: 58714919--58714974 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
58714909 TCAGGTAATT
58714919 TTTGGGTAATTCGGTTAA
1 TTTGGGTAATTCGGTTAA
*
58714937 TTTGGTTAATTCGGTTAA
1 TTTGGGTAATTCGGTTAA
* *
58714955 -TCGGGTAATTCGGGTAA
1 TTTGGGTAATTCGGTTAA
58714972 TTT
1 TTT
58714975 TTAACCAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.21, C:0.07, G:0.27, T:0.45
Consensus pattern (18 bp):
TTTGGGTAATTCGGTTAA
Found at i:58716171 original size:7 final size:7
Alignment explanation
Indices: 58716159--58716192 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
58716149 GATTTAGTCT
58716159 TTTATTA
1 TTTATTA
58716166 TTTATTA
1 TTTATTA
58716173 TTTATTA
1 TTTATTA
58716180 TTTATT-
1 TTTATTA
58716186 TTTATTA
1 TTTATTA
58716193 AATTTGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTA
Found at i:58716796 original size:23 final size:22
Alignment explanation
Indices: 58716764--58716809 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
58716754 GATTTCAATA
*
58716764 TATATATTTTGTATTTTTTTCTT
1 TATATATTTT-TATTTATTTCTT
* *
58716787 TATATTTTTTTGTTTATTTCTT
1 TATATATTTTTATTTATTTCTT
58716809 T
1 T
58716810 CATTTGTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (22 bp):
TATATATTTTTATTTATTTCTT
Found at i:58716931 original size:13 final size:14
Alignment explanation
Indices: 58716897--58716934 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
58716887 TTTTCTTATG
58716897 TATATTAGTTTCGTT
1 TATATTA-TTTCGTT
58716912 TAT-TTATTT-GTT
1 TATATTATTTCGTT
58716924 TATATTATTTC
1 TATATTATTTC
58716935 TATGTCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.66
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:58716961 original size:15 final size:15
Alignment explanation
Indices: 58716941--58716974 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
58716931 TTTCTATGTC
58716941 ATTGTTGTATTTATT
1 ATTGTTGTATTTATT
*
58716956 ATTGTTGTATTTGTT
1 ATTGTTGTATTTATT
58716971 ATTG
1 ATTG
58716975 CGACATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (15 bp):
ATTGTTGTATTTATT
Found at i:58728000 original size:116 final size:116
Alignment explanation
Indices: 58727804--58728014 Score: 300
Period size: 116 Copynumber: 1.8 Consensus size: 116
58727794 ATATATACAT
* * * * *
58727804 TAAATGTCAATTAAATCGATCAGTTCAATTATAAAAATTAATAGCGAATAACAGATCAACTTCAT
1 TAAATGTCAATAAAATCGACCAGTTCAATTATAAAAATTAATAGCGAATAACAAACCAACCTCAT
* * *
58727869 TTGAACTATTTGCAACACAAACTTAACTTCAATTCAATAAAAAATATACCC
66 TTGAACCACTTGCAACACAAACTCAACTTCAATTCAATAAAAAATATACCC
* *
58727920 TAAATGTCAATAAAATCGACCGGTTCAATTATGAAAATTAATAGCGAA-AACCAAACCAACCTCA
1 TAAATGTCAATAAAATCGACCAGTTCAATTATAAAAATTAATAGCGAATAA-CAAACCAACCTCA
58727984 CTTT-AACCACTTGCAACACAAACTCAACTTC
65 -TTTGAACCACTTGCAACACAAACTCAACTTC
58728015 CATAACCCAT
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
115 2 0.02
116 78 0.94
117 3 0.04
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.27
Consensus pattern (116 bp):
TAAATGTCAATAAAATCGACCAGTTCAATTATAAAAATTAATAGCGAATAACAAACCAACCTCAT
TTGAACCACTTGCAACACAAACTCAACTTCAATTCAATAAAAAATATACCC
Found at i:58729048 original size:20 final size:20
Alignment explanation
Indices: 58729012--58729049 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58729002 ACCCTAACTC
*
58729012 GAATCCTAAACTTAAACCTT
1 GAATCCTAAACTCAAACCTT
58729032 GAAT-CTAAACCTCAAACC
1 GAATCCTAAA-CTCAAACC
58729050 CCCAAAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.42, C:0.29, G:0.05, T:0.24
Consensus pattern (20 bp):
GAATCCTAAACTCAAACCTT
Found at i:58731319 original size:16 final size:17
Alignment explanation
Indices: 58731292--58731326 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
58731282 ATATAGCTTT
58731292 TTTTTTAGTTTAAAAAA
1 TTTTTTAGTTTAAAAAA
58731309 TTTTTTA-TTTAAAAAA
1 TTTTTTAGTTTAAAAAA
58731325 TT
1 TT
58731327 GCCTATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTTTTAGTTTAAAAAA
Found at i:58731571 original size:2 final size:2
Alignment explanation
Indices: 58731564--58731596 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
58731554 CATTAACATT
58731564 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58731597 TTATCGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58732806 original size:22 final size:21
Alignment explanation
Indices: 58732779--58732827 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
58732769 CATTTGGTGA
*
58732779 AAATATGTTTGAAA-ATTTTATC
1 AAATAT-TTTCAAACATTTT-TC
58732801 AAATATTTTCAAAGCATTTTTC
1 AAATATTTTCAAA-CATTTTTC
58732823 AAATA
1 AAATA
58732828 CACTCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
22 13 0.54
23 5 0.21
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (21 bp):
AAATATTTTCAAACATTTTTC
Found at i:58735879 original size:21 final size:23
Alignment explanation
Indices: 58735853--58735900 Score: 82
Period size: 21 Copynumber: 2.2 Consensus size: 23
58735843 AATCTGCTAC
58735853 TTTTTGTTGTTG-TTT-TCATTG
1 TTTTTGTTGTTGTTTTGTCATTG
58735874 TTTTTGTTGTTGTTTTGTCATTG
1 TTTTTGTTGTTGTTTTGTCATTG
58735897 TTTT
1 TTTT
58735901 GGTGTCGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 12 0.48
22 3 0.12
23 10 0.40
ACGTcount: A:0.04, C:0.04, G:0.19, T:0.73
Consensus pattern (23 bp):
TTTTTGTTGTTGTTTTGTCATTG
Found at i:58736150 original size:15 final size:16
Alignment explanation
Indices: 58736125--58736157 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
58736115 CTTAATTTTT
58736125 TATATAAAAATAATAA
1 TATATAAAAATAATAA
*
58736141 TATA-AAAAATATTAA
1 TATATAAAAATAATAA
58736156 TA
1 TA
58736158 CGAGCGTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATATAAAAATAATAA
Found at i:58736967 original size:27 final size:27
Alignment explanation
Indices: 58736930--58736982 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
58736920 ACCAAAAATT
58736930 TATTTTAAAAATAAAAAAATAAAAAAAG
1 TATTTTAAAAAT-AAAAAATAAAAAAAG
58736958 TATTTT-AAAATAAAAAATAAAAAAA
1 TATTTTAAAAATAAAAAATAAAAAAA
58736983 AATATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 14 0.56
27 5 0.20
28 6 0.24
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (27 bp):
TATTTTAAAAATAAAAAATAAAAAAAG
Found at i:58736983 original size:27 final size:27
Alignment explanation
Indices: 58736930--58736992 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
58736920 ACCAAAAATT
*
58736930 TATTTTAAAAATAAAAAAATAAAAAAAG
1 TATTTT-AAAATAAAAAAATAAAAAAAA
58736958 TATTTTAAAAT-AAAAAATAAAAAAAAA
1 TATTTTAAAATAAAAAAAT-AAAAAAAA
58736985 TATATTTA
1 TAT-TTTA
58736993 TTATATATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 7 0.22
27 15 0.47
28 10 0.31
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
TATTTTAAAATAAAAAAATAAAAAAAA
Found at i:58738272 original size:31 final size:31
Alignment explanation
Indices: 58738237--58738300 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
58738227 ACATAAACTG
58738237 AATTTCAAATTTTAACATATTAAAGGGACTA
1 AATTTCAAATTTTAACATATTAAAGGGACTA
58738268 AATTTCAAATTTTAACATATTAAAGGGACTA
1 AATTTCAAATTTTAACATATTAAAGGGACTA
58738299 AA
1 AA
58738301 AAGTAAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.34
Consensus pattern (31 bp):
AATTTCAAATTTTAACATATTAAAGGGACTA
Found at i:58740677 original size:6 final size:6
Alignment explanation
Indices: 58740666--58740698 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
58740656 GGATTATGAA
58740666 GATAAT GATAAT GATAAT GATAAT GATAAT GAT
1 GATAAT GATAAT GATAAT GATAAT GATAAT GAT
58740699 TTGGGCATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (6 bp):
GATAAT
Found at i:58742629 original size:3 final size:3
Alignment explanation
Indices: 58742603--58742744 Score: 79
Period size: 3 Copynumber: 46.7 Consensus size: 3
58742593 TATCAATGAA
* * * *
58742603 AAT ATT AAT AAT ATT AAAT AAAT AAT AAT AAT AAT AAT AAT ATT AAC
1 AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** ** * * *
58742650 AAT AATT TAT AAT AAT GTT AAT AGG AAC AA- AAT AAC AAT AAT ACT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * * *
58742695 AAT AAT AAT AAT GCT AGT AAT AAT AAG GAT AAT AAT AGT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
58742743 AA
1 AA
58742745 AAAGGTCAAT
Statistics
Matches: 101, Mismatches: 35, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
2 2 0.02
3 91 0.90
4 8 0.08
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:58745893 original size:2 final size:2
Alignment explanation
Indices: 58745886--58745917 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
58745876 CATACAAAAG
*
58745886 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58745918 GTGTGGGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58747240 original size:15 final size:14
Alignment explanation
Indices: 58747220--58747253 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
58747210 GGGATACTAC
*
58747220 AATTATCTTAATATT
1 AATTATCCTAATA-T
58747235 AATTATCCTAATAT
1 AATTATCCTAATAT
58747249 AATTA
1 AATTA
58747254 AAATAGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTATCCTAATAT
Found at i:58749208 original size:44 final size:44
Alignment explanation
Indices: 58749152--58749242 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
58749142 ACTCTATTTT
* *
58749152 TTAGTTTTCCACTTAAACTCTTATTAGTGTAGGTTATTTTATTA
1 TTAGTTTCCCACTTAAACTCTTATTAGTGTAGGTTATTTTAATA
*
58749196 TTAGTTTCCCACTTAAACTCTTATTAGTTTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTTATTAGTGTAGGTTATTTTAATA
58749240 TTA
1 TTA
58749243 TTTGACCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTTATTAGTGTAGGTTATTTTAATA
Found at i:58750521 original size:41 final size:41
Alignment explanation
Indices: 58750464--58750614 Score: 173
Period size: 41 Copynumber: 3.7 Consensus size: 41
58750454 TTTTGTAAGT
*
58750464 TCAGGCTTTTTGCCTAGCAGGCTTTATGTCAGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGTCAGTGAATTATA
*
58750505 TCAGGCTTTATGCCTAGCAGGC-TCA-GTGCTAGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGT-C-AGTGAATTATA
* * * * *
58750546 TCAGACTTTATGTCTAGCAGGCTTTGTG-CAGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGTCA-GTGAATTATA
* *
58750587 TCGGGCTTTGTGCCTAGCAGGCTTTATG
1 TCAGGCTTTATGCCTAGCAGGCTTTATG
58750615 CCGGTGTTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
39 2 0.02
40 4 0.04
41 84 0.91
42 1 0.01
43 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTTATGTCAGTGAATTATA
Found at i:58751279 original size:2 final size:2
Alignment explanation
Indices: 58751272--58751297 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58751262 GATCTATTTG
58751272 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
58751298 GATGTTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58751527 original size:22 final size:22
Alignment explanation
Indices: 58751502--58751606 Score: 63
Period size: 22 Copynumber: 4.6 Consensus size: 22
58751492 ATATGATGTA
58751502 TTGTGTATATGCTGCCTATTTG
1 TTGTGTATATGCTGCCTATTTG
* * *
58751524 TTGTATATATGCTG-TTAAATT-
1 TTGTGTATATGCTGCCT-ATTTG
*
58751545 TTG-GTATAAAAATGCTGCTCAATTTG
1 TTGTGTAT----ATGCTGC-CTATTTG
* * *
58751571 GTATGTATATGTTGCCTATTTG
1 TTGTGTATATGCTGCCTATTTG
*
58751593 TTGTATATATGCTG
1 TTGTGTATATGCTG
58751607 TTAAATTTTG
Statistics
Matches: 59, Mismatches: 15, Indels: 18
0.64 0.16 0.20
Matches are distributed among these distances:
20 3 0.05
21 4 0.07
22 32 0.54
23 6 0.10
24 6 0.10
25 3 0.05
26 1 0.02
27 4 0.07
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.48
Consensus pattern (22 bp):
TTGTGTATATGCTGCCTATTTG
Found at i:58751574 original size:23 final size:23
Alignment explanation
Indices: 58751544--58751643 Score: 67
Period size: 23 Copynumber: 4.3 Consensus size: 23
58751534 GCTGTTAAAT
58751544 TTTGGTATAAAAATGCTGCTCAA
1 TTTGGTATAAAAATGCTGCTCAA
** * * *
58751567 TTTGGTATGTATATGTTGC-CTA
1 TTTGGTATAAAAATGCTGCTCAA
* * * * * *
58751589 TTTGTTGTATATATGCTGTTAAA
1 TTTGGTATAAAAATGCTGCTCAA
* *
58751612 TTTTGGTGTAAAAATGTTGCTCAA
1 -TTTGGTATAAAAATGCTGCTCAA
58751636 TTTGGTAT
1 TTTGGTAT
58751644 GTATATGCTG
Statistics
Matches: 56, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
22 16 0.29
23 23 0.41
24 17 0.30
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (23 bp):
TTTGGTATAAAAATGCTGCTCAA
Found at i:58751616 original size:69 final size:69
Alignment explanation
Indices: 58751505--58751851 Score: 480
Period size: 69 Copynumber: 5.0 Consensus size: 69
58751495 TGATGTATTG
* * *
58751505 TGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTATAAAAATGCTGCTCAATTT
1 TGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGTTAAATTT
58751570 GGTA
66 GGTA
* * * *
58751574 TGTATATGTTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTT
1 TGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGTTAAATTT
58751639 GGTA
66 GGTA
* * * *
58751643 TGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAGTTTTGGTGTAAAAGTGTTGTTAAATTT
1 TGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGTTAAATTT
58751708 GGTA
66 GGTA
* * * * * *
58751712 TGTATATGCTGCTTAATTGCTGTAAATATGATGTTAAATTTTGGTGTAAAAGTGCTGTTAAATTT
1 TGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGTTAAATTT
58751777 GGTA
66 GGTA
* * * *
58751781 TGTATATGCTGCAC-ATTTGTTGTATATAAGCTGTCCAAATTTTGGTGTATAAATGCTGTTTAAT
1 TGTATATGCTGC-CTATTTGTTGTATATATGCTGT-TAAATTTTGGTGTAAAAATGCTGTTAAAT
58751845 TTGGTA
64 TTGGTA
58751851 T
1 T
58751852 ATATTTGTTG
Statistics
Matches: 249, Mismatches: 27, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
69 217 0.87
70 32 0.13
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (69 bp):
TGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGTTAAATTT
GGTA
Found at i:58754175 original size:21 final size:20
Alignment explanation
Indices: 58754151--58754211 Score: 50
Period size: 24 Copynumber: 2.7 Consensus size: 20
58754141 AAGTATACGT
58754151 ATTTTTTAAATTTTATTTTTA
1 ATTTTTTAAATTTTA-TTTTA
*
58754172 ATTTATTGGGAAATATTTATTTTA
1 ATTT-TT--TAAAT-TTTATTTTA
58754196 ATGTTTTTAATATTTT
1 AT-TTTTTAA-ATTTT
58754212 TGATGTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
21 4 0.12
22 7 0.22
23 2 0.06
24 13 0.41
25 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
ATTTTTTAAATTTTATTTTA
Found at i:58754871 original size:22 final size:24
Alignment explanation
Indices: 58754840--58754883 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
58754830 TTTTGAAAAT
*
58754840 ATTTTTAATT-AA-TATTTTTACA
1 ATTTTAAATTAAATTATTTTTACA
58754862 ATTTTAAATTAAATTATTTTTA
1 ATTTTAAATTAAATTATTTTTA
58754884 AAAATGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 8 0.42
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTTAAATTAAATTATTTTTACA
Found at i:58755802 original size:23 final size:23
Alignment explanation
Indices: 58755776--58755819 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
58755766 ACCCATAATG
58755776 TAATATCCC-GAAAATTACTACTT
1 TAATA-CCCTGAAAATTACTACTT
58755799 TAATACCCTGAAAATTACTAC
1 TAATACCCTGAAAATTACTAC
58755820 AGTAAGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.32
Consensus pattern (23 bp):
TAATACCCTGAAAATTACTACTT
Found at i:58767627 original size:16 final size:15
Alignment explanation
Indices: 58767589--58767632 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
58767579 TACAAAAAAG
*
58767589 AAATTAAACTATGATT
1 AAATTAAA-AATGATT
58767605 AATATTAAAAATGATCT
1 AA-ATTAAAAATGAT-T
58767622 AAATTAAAAAT
1 AAATTAAAAAT
58767633 ATTTATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (15 bp):
AAATTAAAAATGATT
Found at i:58769330 original size:33 final size:33
Alignment explanation
Indices: 58769290--58769411 Score: 185
Period size: 33 Copynumber: 3.8 Consensus size: 33
58769280 ATATGAATTT
58769290 TTTTATGATCTAATTGATGTCAATAATATGAAC
1 TTTTATGATCTAATTGATGTCAATAATATGAAC
58769323 TTTTATGATCTAATTGATGTCAATAATATGAAC
1 TTTTATGATCTAATTGATGTCAATAATATGAAC
* **
58769356 TTTTATGATCTAATTGATG-AAAT-ATATGAGT
1 TTTTATGATCTAATTGATGTCAATAATATGAAC
* *
58769387 TTTTATGATATAATTGATATCAATA
1 TTTTATGATCTAATTGATGTCAATA
58769412 TTAAGTGTTT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
31 23 0.28
32 6 0.07
33 52 0.64
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (33 bp):
TTTTATGATCTAATTGATGTCAATAATATGAAC
Found at i:58769401 original size:64 final size:66
Alignment explanation
Indices: 58769290--58769411 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 66
58769280 ATATGAATTT
* * *
58769290 TTTTATGATCTAATTGATGTCAATAATATGAACTTTTATGATCTAATTGATGTCAATAATATGAA
1 TTTTATGATCTAATTGATGTAAATAATATGAACTTTTATGATATAATTGATATCAATAATATGAA
58769355 C
66 C
**
58769356 TTTTATGATCTAATTGATG-AAAT-ATATGAGTTTTTATGATATAATTGATATCAATA
1 TTTTATGATCTAATTGATGTAAATAATATGAACTTTTATGATATAATTGATATCAATA
58769412 TTAAGTGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 29 0.57
65 3 0.06
66 19 0.37
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (66 bp):
TTTTATGATCTAATTGATGTAAATAATATGAACTTTTATGATATAATTGATATCAATAATATGAA
C
Found at i:58769571 original size:33 final size:34
Alignment explanation
Indices: 58769527--58769615 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 34
58769517 ATATATAAAT
*
58769527 TTTTTAAGATCTAATTGATGTCAATA-ATATGAA
1 TTTTTATGATCTAATTGATGTCAATAGATATGAA
* * *
58769560 TTTTTATGATCTGATTAATG--AA-AGATATGAG
1 TTTTTATGATCTAATTGATGTCAATAGATATGAA
* * *
58769591 TCTTTATGATATAATTGATATCAAT
1 TTTTTATGATCTAATTGATGTCAAT
58769616 TGTAAGTGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
30 1 0.02
31 23 0.53
33 19 0.44
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (34 bp):
TTTTTATGATCTAATTGATGTCAATAGATATGAA
Found at i:58769685 original size:205 final size:205
Alignment explanation
Indices: 58769323--58769772 Score: 744
Period size: 205 Copynumber: 2.2 Consensus size: 205
58769313 TAATATGAAC
* * * *
58769323 TTTTATGATCTAATTGATGTCAATAATATGAACTTTTATGATCTAATTGATGAAATATATGAGTT
1 TTTTATGATCTAATTGATGTCAATAATATGAATTTTTATGATCTAATTAATGAAAGATATGAGTC
58769388 TTTATGATATAATTGATATCAATATTAAGTGTTTTTTCCCCTTCCAATTCTAGGTGCATTTGTAT
66 TTTATGATATAATTGATATCAATATTAAGTGTTTTTTCCCCTTCCAATTCTAGGTGCATTTGTAT
58769453 GGATCATGCATGCTTTTTAGCTCATCCCTTGTTATATGAGTTAGTATTGAGTAGAATGAATGAAA
131 GGATCATGCATGCTTTTTAGCTCATCCCTTGTTATATGAGTTAGTATTGAGTAGAATGAATGAAA
58769518 TATATAAATT
196 TATATAAATT
* *
58769528 TTTTAAGATCTAATTGATGTCAATAATATGAATTTTTATGATCTGATTAATGAAAGATATGAGTC
1 TTTTATGATCTAATTGATGTCAATAATATGAATTTTTATGATCTAATTAATGAAAGATATGAGTC
58769593 TTTATGATATAATTGATATCAAT-TGTAAGTGTTTTTTCCCCTTCCAATTCTAGGTGCATTTGTA
66 TTTATGATATAATTGATATCAATAT-TAAGTGTTTTTTCCCCTTCCAATTCTAGGTGCATTTGTA
* ** * *
58769657 TGTATTGTGCATGCTTTTTAGTTCATCCCTTGTTATATGAGTTAGTATTTAGTAGAATGAATGAA
130 TGGATCATGCATGCTTTTTAGCTCATCCCTTGTTATATGAGTTAGTATTGAGTAGAATGAATGAA
*
58769722 ATATATGAATT
195 ATATATAAATT
* *
58769733 TTTTATGATCTAATTGATG-AAAT-ATATGAGTTTTTATGAT
1 TTTTATGATCTAATTGATGTCAATAATATGAATTTTTATGAT
58769773 ACAATTGATG
Statistics
Matches: 229, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
203 16 0.07
204 4 0.02
205 209 0.91
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (205 bp):
TTTTATGATCTAATTGATGTCAATAATATGAATTTTTATGATCTAATTAATGAAAGATATGAGTC
TTTATGATATAATTGATATCAATATTAAGTGTTTTTTCCCCTTCCAATTCTAGGTGCATTTGTAT
GGATCATGCATGCTTTTTAGCTCATCCCTTGTTATATGAGTTAGTATTGAGTAGAATGAATGAAA
TATATAAATT
Found at i:58769770 original size:31 final size:32
Alignment explanation
Indices: 58769717--58769782 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
58769707 AGTAGAATGA
*
58769717 ATGAAATATATGAATTTTTTATGAT-CTAATTG
1 ATGAAATATATGAAGTTTTTATGATAC-AATTG
58769749 ATGAAATATATG-AGTTTTTATGATACAATTG
1 ATGAAATATATGAAGTTTTTATGATACAATTG
58769780 ATG
1 ATG
58769783 TCAATTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 19 0.59
32 13 0.41
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (32 bp):
ATGAAATATATGAAGTTTTTATGATACAATTG
Found at i:58769893 original size:171 final size:172
Alignment explanation
Indices: 58769553--58769922 Score: 516
Period size: 172 Copynumber: 2.2 Consensus size: 172
58769543 GATGTCAATA
* * *
58769553 ATATGAA-TTTTTATGATCTGATTAATGAAAGATATGAGTCTTTATGATATAATTGATATCAATT
1 ATATGAATTTTTTATGATCTAATTGATGAAAGATATGAGTCTTTATGATACAATTGATATCAATT
* ** * * *
58769617 GTAAGTGTTTTTTCCCCTTCCAATTCTAGGTGCATTTGTATGTATTGTGCATGCTTTTTAGTTCA
66 ATAAGACTTTTCTCCCCTTCCAATTCTAGGTGCATTTGTATGGATTGTGCATGCTTTTTAGCTCA
**
58769682 TCCCTTGTTATATGAGTTAGTATTTAGTAGAATGAATGAAAT
131 TCCCTTGTTATATGAGTTAGTACCTAGTAGAATGAATGAAAT
* * *
58769724 ATATGAATTTTTTATGATCTAATTGATGAAATATATGAGTTTTTATGATACAATTGATGTCAATT
1 ATATGAATTTTTTATGATCTAATTGATGAAAGATATGAGTCTTTATGATACAATTGATATCAATT
*
58769789 ATATAGACTTTTCT-CCCTTCCCATTCTAGGTGCATTTGTGA-GGA-TGATGCATGC-TTTTAGC
66 ATA-AGACTTTTCTCCCCTTCCAATTCTAGGTGCATTTGT-ATGGATTG-TGCATGCTTTTTAGC
*
58769850 TCATCCCTTGTTATATGAGTTAGTACCTAGTAGAATTAATGAAAT
128 TCATCCCTTGTTATATGAGTTAGTACCTAGTAGAATGAATGAAAT
* *
58769895 ATATGGATTTTTTATGATCTAAGTGATG
1 ATATGAATTTTTTATGATCTAATTGATG
58769923 TCAATTATAT
Statistics
Matches: 177, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
171 83 0.47
172 86 0.49
173 8 0.05
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (172 bp):
ATATGAATTTTTTATGATCTAATTGATGAAAGATATGAGTCTTTATGATACAATTGATATCAATT
ATAAGACTTTTCTCCCCTTCCAATTCTAGGTGCATTTGTATGGATTGTGCATGCTTTTTAGCTCA
TCCCTTGTTATATGAGTTAGTACCTAGTAGAATGAATGAAAT
Found at i:58775624 original size:153 final size:158
Alignment explanation
Indices: 58775414--58775721 Score: 410
Period size: 153 Copynumber: 2.0 Consensus size: 158
58775404 CGTGGTGTAG
*
58775414 GGATGTCAGTGGAATATGTGCTATTGAAATCCTTTGTGTATATATATCAACCTATGACCATTGTT
1 GGATGTCAGTGGAATA-GTGCTATTGAAATCCTTTGTGTATATATATCAACCTATGACCATCGTT
* * * ** * * *
58775479 AAAGTAGTGTGATAGGAGGGTATTTTTTGCAATTCCTCAGGGACGTATGCCTCTGCCCCTTGGAA
65 AAAGTAGTATGATAGGAGGGTATTTTTGGCAATTCCTCAGGGACATACACATCGGCCCCTTAGAA
*
58775544 GTTTTCAGTGGTTTATGGATGAACTAGTT
130 GTTTTCAGTGATTTATGGATGAACTAGTT
* *
58775573 GGATGTCAGTGG-A-A-TGCTGTTGAAATCC-TT-TGTATATATATCGACCTATGACCATCGTTA
1 GGATGTCAGTGGAATAGTGCTATTGAAATCCTTTGTGTATATATATCAACCTATGACCATCGTTA
* * * * *
58775633 GAGTAGTATTATAGGAGGGTATTTTTGGCAATTCGTCAGGGACATACACATCGGGCCCTTAGAGG
66 AAGTAGTATGATAGGAGGGTATTTTTGGCAATTCCTCAGGGACATACACATCGGCCCCTTAGAAG
*
58775698 TTTTTAGTGATTTATGGATGAACT
131 TTTTCAGTGATTTATGGATGAACT
58775722 GGTTCCTGAT
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
153 102 0.78
154 2 0.02
155 13 0.10
157 1 0.01
158 1 0.01
159 12 0.09
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (158 bp):
GGATGTCAGTGGAATAGTGCTATTGAAATCCTTTGTGTATATATATCAACCTATGACCATCGTTA
AAGTAGTATGATAGGAGGGTATTTTTGGCAATTCCTCAGGGACATACACATCGGCCCCTTAGAAG
TTTTCAGTGATTTATGGATGAACTAGTT
Found at i:58783041 original size:15 final size:14
Alignment explanation
Indices: 58783008--58783046 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
58782998 ATTTGATTGA
58783008 AAAATGACTTCTAG
1 AAAATGACTTCTAG
*
58783022 AAAATGATTTCTAG
1 AAAATGACTTCTAG
58783036 ACAAATGACTT
1 A-AAATGACTT
58783047 ACTTTTCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (14 bp):
AAAATGACTTCTAG
Found at i:58785119 original size:71 final size:70
Alignment explanation
Indices: 58785002--58785137 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 70
58784992 GAATTTGAGG
* * *
58785002 TTTAACTTAGTTGATCTTGTGAGTAGGAATTTTGAAACTTAATGGACCAAAAAAGTAAACAAAAC
1 TTTAACTCAGTTGATCTCGTGAGTAGGAATGTTGAAACTTAATGGACCAAAAAAGTAAACAAAAC
58785067 TTGGA
66 TTGGA
* * * *
58785072 TTTAACTCGGTTGATTCTCGTGAGTAGGAATGTTGAAACTTAGTGGACCAGAAAAGTAAATAAAA
1 TTTAACTCAGTTGA-TCTCGTGAGTAGGAATGTTGAAACTTAATGGACCAAAAAAGTAAACAAAA
58785137 C
65 C
58785138 GAGTCTTCGG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
70 12 0.21
71 46 0.79
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (70 bp):
TTTAACTCAGTTGATCTCGTGAGTAGGAATGTTGAAACTTAATGGACCAAAAAAGTAAACAAAAC
TTGGA
Found at i:58785249 original size:83 final size:84
Alignment explanation
Indices: 58785091--58785249 Score: 203
Period size: 83 Copynumber: 1.9 Consensus size: 84
58785081 GTTGATTCTC
* * * * * * **
58785091 GTGAGTAGGAATGTTGAAACTTAGTGGACCAGAAAAGTAAATAAAACGAGTCTTCGGATTTGGAG
1 GTGAGTAAGAATATTGAAACTTAGTGAACCAGAAAAATAAATAAAACAAATCTTCAAATTTGGAG
*
58785156 TTTAATTTAATAGGTTCCT
66 TTTAACTTAATAGGTTCCT
* * *
58785175 GTGAGTAAGAATATTGAAATTTAGTGAACCA-AAAAATAAATAAAACAAATTTTCAAATTTGGGG
1 GTGAGTAAGAATATTGAAACTTAGTGAACCAGAAAAATAAATAAAACAAATCTTCAAATTTGGAG
58785239 TTTAACTTAAT
66 TTTAACTTAAT
58785250 TGATTCTGGT
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
83 36 0.57
84 27 0.43
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.31
Consensus pattern (84 bp):
GTGAGTAAGAATATTGAAACTTAGTGAACCAGAAAAATAAATAAAACAAATCTTCAAATTTGGAG
TTTAACTTAATAGGTTCCT
Found at i:58785514 original size:109 final size:109
Alignment explanation
Indices: 58785401--58785668 Score: 378
Period size: 109 Copynumber: 2.5 Consensus size: 109
58785391 TTAGAGTTAC
* * * *
58785401 TCCATTTGATTTATTAATATGATTATTTGAATACACTCGTATTTCAATTTACGTTAATGCTTTAT
1 TCCATTTGATTTATTAATATGATTATTTGAACACACTAGTATTTCAATTTACATTAATGCCTTAT
* * *
58785466 TTGGGAAGGCAACAATGTATTGTAGCAATTGTGTCTAGGTTTAG
66 TTGAGAAGGCAACAAAGTATTGTAGCAATTGTGTCTAGGCTTAG
* * *
58785510 TCCATTTGATTTACTAATATGATCATTTGAACACACTAGTATTTCAATTTATATTAATGCCTTAT
1 TCCATTTGATTTATTAATATGATTATTTGAACACACTAGTATTTCAATTTACATTAATGCCTTAT
* *
58785575 TTGAGAGGGCAACAAAGTATTGTGGCAATTGTGTCTAGGCTTAG
66 TTGAGAAGGCAACAAAGTATTGTAGCAATTGTGTCTAGGCTTAG
* * *
58785619 CCCATTT-AGTTTATTAATATGATTATTT-AACACCCTTGTATTTCAATTTA
1 TCCATTTGA-TTTATTAATATGATTATTTGAACACACTAGTATTTCAATTTA
58785669 TGGTAGTTGT
Statistics
Matches: 141, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
108 21 0.15
109 120 0.85
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (109 bp):
TCCATTTGATTTATTAATATGATTATTTGAACACACTAGTATTTCAATTTACATTAATGCCTTAT
TTGAGAAGGCAACAAAGTATTGTAGCAATTGTGTCTAGGCTTAG
Found at i:58785681 original size:72 final size:73
Alignment explanation
Indices: 58785603--58785741 Score: 199
Period size: 72 Copynumber: 1.9 Consensus size: 73
58785593 ATTGTGGCAA
* *
58785603 TTGTGTCTAGGCTTAGCCCATTTAGTTTATTAATATGATTATTT-AACACCCTTGTATTTCAATT
1 TTGTGTCTAGGCTTAGCCCATTTAGTTTATTAATATGATCATTTGAACACCCTCGTATTTCAATT
58785667 TATGGTAG
66 TATGGTAG
* * * ** *
58785675 TTGTGTCTAGGTTTAGCCCATTTGGTTTATTATTATGATCATTTGAACATGCTCGTATTTTAATT
1 TTGTGTCTAGGCTTAGCCCATTTAGTTTATTAATATGATCATTTGAACACCCTCGTATTTCAATT
58785740 TA
66 TA
58785742 CGTTAACGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 40 0.69
73 18 0.31
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (73 bp):
TTGTGTCTAGGCTTAGCCCATTTAGTTTATTAATATGATCATTTGAACACCCTCGTATTTCAATT
TATGGTAG
Found at i:58785874 original size:26 final size:26
Alignment explanation
Indices: 58785845--58785900 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
58785835 TCAAATGATT
58785845 AATATTAAATCGATCGGAAAATTAAG
1 AATATTAAATCGATCGGAAAATTAAG
58785871 AATATTAAATCGATCGGAAAATTAAG
1 AATATTAAATCGATCGGAAAATTAAG
58785897 AATA
1 AATA
58785901 GGATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (26 bp):
AATATTAAATCGATCGGAAAATTAAG
Found at i:58802810 original size:80 final size:82
Alignment explanation
Indices: 58802661--58802817 Score: 255
Period size: 80 Copynumber: 1.9 Consensus size: 82
58802651 TAGGAAGGGC
* * *
58802661 TATGTTTATGAGTTACATCTCTAATGATCTACTCAAAAAAAAACTTGGCTATTTTTTAAAAAGAT
1 TATGTTTATAAGTTACATCTCTAATGATCTACTCAAAAAAAAACTTGGCTATTGTATAAAAAGAT
58802726 ATTTAGAATTCAAAAGT
66 ATTTAGAATTCAAAAGT
* *
58802743 TATGTTTATAAGTTGCATCTCTAATGATCTA-T-TAAAAAAAACTTGGCTATTGTATAAAAAGAT
1 TATGTTTATAAGTTACATCTCTAATGATCTACTCAAAAAAAAACTTGGCTATTGTATAAAAAGAT
58802806 ATTTAGAATTCA
66 ATTTAGAATTCA
58802818 GCAAATGAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
80 40 0.57
81 1 0.01
82 29 0.41
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Consensus pattern (82 bp):
TATGTTTATAAGTTACATCTCTAATGATCTACTCAAAAAAAAACTTGGCTATTGTATAAAAAGAT
ATTTAGAATTCAAAAGT
Found at i:58807356 original size:19 final size:21
Alignment explanation
Indices: 58807332--58807371 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
58807322 AGCATAAATT
58807332 ATATAATATA-TAT-AACATA
1 ATATAATATATTATAAACATA
58807351 ATATAATATATTATAAACATA
1 ATATAATATATTATAAACATA
58807372 GAAAATGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAATATATTATAAACATA
Found at i:58808770 original size:6 final size:6
Alignment explanation
Indices: 58808759--58808788 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
58808749 TTAATGATTT
58808759 AATATA AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA
58808789 TAATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:58812575 original size:20 final size:20
Alignment explanation
Indices: 58812520--58812560 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
58812510 CTGAACCCTG
*
58812520 AATCTCGAACTCT-AACTCA
1 AATCTCGAACCCTAAACTCA
58812539 AATCTCGAACCCTAAACTCA
1 AATCTCGAACCCTAAACTCA
58812559 AA
1 AA
58812561 CTCTGAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (20 bp):
AATCTCGAACCCTAAACTCA
Done.