Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 23
Found at i:526926 original size:17 final size:18
Alignment explanation
Indices: 526904--526946 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
526894 ATATATCCGG
526904 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
526921 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
526941 TATCAT
1 TATCAT
526947 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:526964 original size:20 final size:19
Alignment explanation
Indices: 526909--526955 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
526899 TCCGGTATCA
526909 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
526928 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
526949 TTTTACC
1 TTTTACC
526956 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:527116 original size:20 final size:20
Alignment explanation
Indices: 527089--527135 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
527079 TCCGGTAACG
527089 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
527108 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
527129 TTTTACC
1 TTTTACC
527136 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:527299 original size:181 final size:181
Alignment explanation
Indices: 526876--527346 Score: 696
Period size: 181 Copynumber: 2.6 Consensus size: 181
526866 CGTACTTACG
* * *
526876 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
526941 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
527005 AGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
527056 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
527121 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
527186 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * *
527238 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACC-GTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
527301 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
527347 AATTTGGATC
Statistics
Matches: 263, Mismatches: 25, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
180 97 0.37
181 130 0.49
182 36 0.14
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:527810 original size:228 final size:227
Alignment explanation
Indices: 527413--527896 Score: 841
Period size: 228 Copynumber: 2.1 Consensus size: 227
527403 ACCTACTTTT
*
527413 ATAAGTA-TGTACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTC
1 ATAAGTATTG-ACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTC
527477 AATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
65 AATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
527542 ATATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAA-TTTAAATTTAACAATATTAA
130 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA-AATTTTAAATTTAACAATATTAA
* *
527606 CCAAATATAATAATAAATATGTTTTCAACAGTGAA
194 CCAAAGATAATAATAAATATATTTTC-ACAGTGAA
527641 ATAAGTATTGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATTGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
*
527706 ATTTTTTTAATAGTGTTTCAT-TTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
66 A-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
527770 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAAATTTTAAATTTAACAATATTAAC
130 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAAATTTTAAATTTAACAATATTAAC
*
527835 TAAAGATAATAATAAATATATTTTCACAGTGAA
195 CAAAGATAATAATAAATATATTTTCACAGTGAA
*
527868 ATAAGTATGGACACTTTTAT-AAAATGATA
1 ATAAGTATTGACACTTTTATAAAAATGATA
527897 GATAATTTAC
Statistics
Matches: 246, Mismatches: 7, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
226 9 0.04
227 29 0.12
228 187 0.76
229 21 0.09
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (227 bp):
ATAAGTATTGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
ATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAAA
AATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAAATTTTAAATTTAACAATATTAACC
AAAGATAATAATAAATATATTTTCACAGTGAA
Found at i:530270 original size:36 final size:35
Alignment explanation
Indices: 530223--530290 Score: 118
Period size: 36 Copynumber: 1.9 Consensus size: 35
530213 TTGGTTTTTC
*
530223 GAAAATGAATTATTGGAATTTGAATTACTGGAACTG
1 GAAAATGAATTACTGGAATTTGAATTA-TGGAACTG
530259 GAAAATGAATTACTGGAATTTGAATTATGGAA
1 GAAAATGAATTACTGGAATTTGAATTATGGAA
530291 AATGAATTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.32
Consensus pattern (35 bp):
GAAAATGAATTACTGGAATTTGAATTATGGAACTG
Found at i:530296 original size:14 final size:15
Alignment explanation
Indices: 530255--530300 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
530245 AATTACTGGA
530255 ACTGGAAAATGAATT
1 ACTGGAAAATGAATT
**
530270 ACTGGAATTTGAATT
1 ACTGGAAAATGAATT
530285 A-TGGAAAATGAATT
1 ACTGGAAAATGAATT
530299 AC
1 AC
530301 ATTTATGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:530552 original size:48 final size:50
Alignment explanation
Indices: 530456--530553 Score: 114
Period size: 48 Copynumber: 2.0 Consensus size: 50
530446 TACAAATATT
*
530456 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * *
530506 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TT-ATTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
530554 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 21 0.50
49 13 0.31
50 8 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:530726 original size:28 final size:29
Alignment explanation
Indices: 530694--530856 Score: 106
Period size: 30 Copynumber: 5.6 Consensus size: 29
530684 AAAATATAAT
530694 TTAAATATATAAATAA-TATTAT-TCATTA
1 TTAAATATATAAATAATTATTATAT-ATTA
*
530722 TTAAATATATAAAAAATTTATTATATATTA
1 TTAAATATATAAATAA-TTATTATATATTA
* *
530752 TTAAA-ATAAAAATATAATATCT-TATATTA
1 TTAAATATATAAATA-ATTAT-TATATATTA
* * * *
530781 TTATA-ATATAATTGATTATTTTATATAATA
1 TTAAATATATAAATAATTA--TTATATATTA
* *
530811 TTAAAAATATAATATTATATTATTATA-AATA
1 TTAAATATATAA-A-TA-ATTATTATATATTA
*
530842 TT-AATAAATAAATAA
1 TTAAATATATAAATAA
530857 ATAATATTTT
Statistics
Matches: 108, Mismatches: 15, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
27 1 0.01
28 20 0.19
29 29 0.27
30 35 0.32
31 13 0.12
32 5 0.05
33 1 0.01
34 4 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (29 bp):
TTAAATATATAAATAATTATTATATATTA
Found at i:530732 original size:30 final size:27
Alignment explanation
Indices: 530694--530751 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
530684 AAAATATAAT
*
530694 TTAAATATATAAATAATATTATTCAT-TA
1 TTAAATATATAAAAAAT-TTATT-ATATA
530722 TTAAATATATAAAAAATTTATTATATA
1 TTAAATATATAAAAAATTTATTATATA
530749 TTA
1 TTA
530752 TTAAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 2 0.07
27 10 0.36
28 16 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAATATATAAAAAATTTATTATATA
Found at i:530829 original size:22 final size:23
Alignment explanation
Indices: 530804--530847 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
530794 GATTATTTTA
530804 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
530826 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
530848 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:530847 original size:59 final size:61
Alignment explanation
Indices: 530687--530849 Score: 143
Period size: 54 Copynumber: 2.8 Consensus size: 61
530677 CCTTATTAAA
* * *
530687 ATATAAT-TTAAATATATAAATAATATTATTCATTATTAAATATATAA-AAAATTTATTATATAT
1 ATATAATATTAAAAATAT-AATATTA-TATT-ATTA-TAAATAT-TAATAAAATTGATTATATAT
530750 T
61 T
* *
530751 AT-TAA-AATAAAAATATAATATCT-TA-TATTAT---TA-TAATATAATTGATTAT-T-TT
1 ATATAATATTAAAAATATAATAT-TATATTATTATAAATATTAATAAAATTGATTATATATT
530803 ATATAATATTAAAAATATAATATTATATTATTATAAATATTAATAAA
1 ATATAATATTAAAAATATAATATTATATTATTATAAATATTAATAAA
530850 TAAATAAATA
Statistics
Matches: 81, Mismatches: 7, Indels: 27
0.70 0.06 0.23
Matches are distributed among these distances:
52 4 0.05
53 8 0.10
54 27 0.33
55 8 0.10
58 3 0.04
59 10 0.12
60 1 0.01
61 2 0.02
62 4 0.05
63 12 0.15
64 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (61 bp):
ATATAATATTAAAAATATAATATTATATTATTATAAATATTAATAAAATTGATTATATATT
Found at i:533221 original size:62 final size:62
Alignment explanation
Indices: 533150--533273 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
533140 GGAAACAAAG
*
533150 ATATACATTCTAAACTAATGATACACACTATAAACAGAATATATTGAACATATATTCTAACA
1 ATATACATTCTAAACTAATGATACAAACTATAAACAGAATATATTGAACATATATTCTAACA
533212 ATATACATTCTAAACTAATGATACAAACTATAAACAGAATATATTGAACATATATTCTAACA
1 ATATACATTCTAAACTAATGATACAAACTATAAACAGAATATATTGAACATATATTCTAACA
533274 GCAACACCTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (62 bp):
ATATACATTCTAAACTAATGATACAAACTATAAACAGAATATATTGAACATATATTCTAACA
Found at i:535908 original size:32 final size:32
Alignment explanation
Indices: 535813--535909 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
535803 TATATGTATC
*
535813 ACATGTCATGCCATCATTTTAGATGACATGAT
1 ACATGTCATGCCATCATCTTAGATGACATGAT
* ** * * *
535845 ACATATCATATCAACA-CCTAGAGTGATATGAT
1 ACATGTCATGCCATCATCTTAGA-TGACATGAT
*
535877 ACATGTCATGCCATCATCTTGGATGACATGAT
1 ACATGTCATGCCATCATCTTAGATGACATGAT
535909 A
1 A
535910 TATGACGTAC
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
31 4 0.08
32 41 0.84
33 4 0.08
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (32 bp):
ACATGTCATGCCATCATCTTAGATGACATGAT
Found at i:537093 original size:11 final size:11
Alignment explanation
Indices: 537077--537106 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
537067 CCTCTTCATT
537077 CAAACACAAAC
1 CAAACACAAAC
537088 CAAACACAAAC
1 CAAACACAAAC
537099 CAAACACA
1 CAAACACA
537107 TACATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.37, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAACACAAAC
Found at i:539402 original size:30 final size:30
Alignment explanation
Indices: 539366--539424 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
539356 CCGAAGGACA
*
539366 TATCCAGAGGTCATAGAGATCCTCGGTAAC
1 TATCCAGAGGTCATAAAGATCCTCGGTAAC
* * *
539396 TATCCAGGGGTTATAAAGATCCTTGGTAA
1 TATCCAGAGGTCATAAAGATCCTCGGTAA
539425 TTGTCCATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (30 bp):
TATCCAGAGGTCATAAAGATCCTCGGTAAC
Found at i:539461 original size:31 final size:31
Alignment explanation
Indices: 539426--539487 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
539416 CCTTGGTAAT
*
539426 TGTCCATAGGTCCCGAAGAACCTAGGTAAAC
1 TGTCCATAGGTCCCGAAGAACATAGGTAAAC
* * **
539457 TGTCCATATGTTCCTTAGAACATAGGTAAAC
1 TGTCCATAGGTCCCGAAGAACATAGGTAAAC
539488 CCTCGACTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (31 bp):
TGTCCATAGGTCCCGAAGAACATAGGTAAAC
Found at i:544780 original size:30 final size:30
Alignment explanation
Indices: 544744--544816 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
544734 CCCGAAGAAC
*
544744 CTATCCAGAGGTCATAGAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
544774 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
544804 CTGTCCATAGGTC
1 CTATCCAGAGGTC
544817 CCGAATAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:547428 original size:14 final size:15
Alignment explanation
Indices: 547402--547430 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
547392 TTTATTTAAC
547402 TATTAACTTTTTATT
1 TATTAACTTTTTATT
547417 TATTAA-TTTTTATT
1 TATTAACTTTTTATT
547431 ACTTAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTAACTTTTTATT
Found at i:550372 original size:18 final size:18
Alignment explanation
Indices: 550345--550385 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 18
550335 ATATTTTCAA
550345 ATAATCATATATAAAATAAAT
1 ATAAT-ATA-ATAAAA-AAAT
550366 ATAATATAATAAAAAAAT
1 ATAATATAATAAAAAAAT
550384 AT
1 AT
550386 CTTACAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 3 0.15
21 5 0.25
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATATAATAAAAAAAT
Found at i:554088 original size:38 final size:38
Alignment explanation
Indices: 554037--554112 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
554027 CTGCTCGTAC
554037 GCAATGAAGAGGTCTGGTCGTCTAAGGGTGACACGGCT
1 GCAATGAAGAGGTCTGGTCGTCTAAGGGTGACACGGCT
554075 GCAATGAAGAGGTCTGGTCGTCTAAGGGTGACACGGCT
1 GCAATGAAGAGGTCTGGTCGTCTAAGGGTGACACGGCT
554113 CCTACGTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (38 bp):
GCAATGAAGAGGTCTGGTCGTCTAAGGGTGACACGGCT
Found at i:554350 original size:46 final size:45
Alignment explanation
Indices: 554078--554499 Score: 287
Period size: 46 Copynumber: 9.4 Consensus size: 45
554068 CACGGCTGCA
* * *
554078 ATGAAGAGGTCTGGTCGTCTAAGG-G-TGACACGGCTCCTACGTG
1 ATGAAGAGATCTGGTCATCTAAGGTGATAACACGGCTCCTACGTG
* * * *
554121 ATGAGGAAATCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTG
1 ATGAAGAGATCTGGTCATC--T---AA-GGTGATAACACGGCTCCTACGTG
* * * * * *
554172 ATGAGGACG-GCTGGTTATCCTAA--TGTTGACACGGCTCTTACGTG
1 ATGAAGA-GATCTGGTCAT-CTAAGGTGATAACACGGCTCCTACGTG
* * *
554216 ATGAAGAGATCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTG
1 ATGAAGAGATCTGGTCATCT-AAGGTGATAACACGGCTCCTACGTG
* * * * * *
554262 ATGAGGACG-GCTGGTTATCCTAA--TGTTGACACGGCTCTTACGTG
1 ATGAAGA-GATCTGGTCAT-CTAAGGTGATAACACGGCTCCTACGTG
* *
554306 ATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 ATGAAGAGATCTGGTCATCT-AAGGTGATAACACGGCTCCTACGTG
* * * * *
554352 ATGAAGACG-GCTGGTTATCTATGGT--TGACACGGCTCATACGTG
1 ATGAAGA-GATCTGGTCATCTAAGGTGATAACACGGCTCCTACGTG
* *
554395 ATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 ATGAAGAGATCTGGTCATCT-AAGGTGATAACACGGCTCCTACGTG
* * * * *
554441 ATGAAGACG-GCTGGTTATCTATGGT--TGACACGGCTCATACGTG
1 ATGAAGA-GATCTGGTCATCTAAGGTGATAACACGGCTCCTACGTG
554484 ATGAAGAGATCTGGTC
1 ATGAAGAGATCTGGTC
554500 CGGGGGATGA
Statistics
Matches: 288, Mismatches: 64, Indels: 54
0.71 0.16 0.13
Matches are distributed among these distances:
42 2 0.01
43 78 0.27
44 64 0.22
45 9 0.03
46 92 0.32
47 7 0.02
48 2 0.01
49 2 0.01
50 2 0.01
51 29 0.10
52 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (45 bp):
ATGAAGAGATCTGGTCATCTAAGGTGATAACACGGCTCCTACGTG
Found at i:554428 original size:89 final size:90
Alignment explanation
Indices: 554103--554497 Score: 609
Period size: 90 Copynumber: 4.4 Consensus size: 90
554093 CGTCTAAGGG
* * * * *
554103 TGACACGGCTCCTACGTGATGAGGAAATCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATC--TA--AA-GGTGATAACACGGTTCCTA
*
554168 CGTGATGAGGACGGCTGGTTATCCTAATGT
61 CGTGATGAAGACGGCTGGTTATCCTAATGT
* *
554198 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
*
554263 TGAGGACGGCTGGTTATCCTAATGT
66 TGAAGACGGCTGGTTATCCTAATGT
*
554288 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
554353 TGAAGACGGCTGGTTAT-CT-ATGGT
66 TGAAGACGGCTGGTTATCCTAAT-GT
554377 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
554442 TGAAGACGGCTGGTTAT-CT-ATGGT
66 TGAAGACGGCTGGTTATCCTAAT-GT
554466 TGACACGGCTCATACGTGATGAAGAGATCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
554498 TCCGGGGGAT
Statistics
Matches: 290, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
88 2 0.01
89 124 0.43
90 127 0.44
91 2 0.01
93 2 0.01
95 33 0.11
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (90 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
TGAAGACGGCTGGTTATCCTAATGT
Found at i:554461 original size:135 final size:134
Alignment explanation
Indices: 554099--554623 Score: 339
Period size: 135 Copynumber: 3.9 Consensus size: 134
554089 TGGTCGTCTA
* * * * *
554099 AGGG-TGACACGGCTCCTACGTGATGAGGAAA-TCTGGTCATCTTTAGGAAGGGTGATAACTCGG
1 AGGGATGACACGGCTCATACATGATGA-AAAACTCTGGCCATC-TTA-GAAGGGTGATAACACGG
* * * *
554162 TTCCTACGTGATGAGGACGGCTGGTTATCCTAATGT-TGACACGGCTCTTACGTGATGAAGAGAT
63 TTCCTACGTGATGAAGACGGCTGGTTAT-CTAAGGTGTGACACGGCTCCTACGTGATGAAGAGAG
**
554226 CTGGCCATCTAA
127 CTGG---TC-CG
* * * * * ** * ** * * * *
554238 AGGTGATAACATGGTTCCTACGTGATG-AGGACGGCTGGTTATCCT--AA---TGTTGACACGGC
1 AGG-GATGACACGGCTCATACATGATGAAAAAC-TCTGGCCATCTTAGAAGGGTGATAACACGGT
* * ** * *
554297 TCTTACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAAGACG
64 TCCTACGTGATGAAGACG-GCTGGTTATCT-AAGGTG-TGACACGGCTCCTACGTGATGAAGA-G
* *
554361 -GCTGGTTATCT
125 AGCTGG-T-CCG
* * * *
554372 ATGGTTGACACGGCTCATACGTGATGAAGAGA-TCTGGCCATC-TA-AA-GGTGATAACACGGTT
1 AGGGATGACACGGCTCATACATGATGAA-AAACTCTGGCCATCTTAGAAGGGTGATAACACGGTT
* * *
554433 CCTACGTGATGAAGACGGCTGGTTATCTATGGT-TGACACGGCTCATACGTGATGAAGAGATCTG
65 CCTACGTGATGAAGACGGCTGGTTATCTAAGGTGTGACACGGCTCCTACGTGATGAAGAGAGCTG
554497 GTCCG
130 GTCCG
* * *
554502 GGGGATGACACGGTTCATACATGATGAAAAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGT
1 AGGGATGACACGGCTCATACATGATGAAAAACTCTGGCCATC-TTA-GAAGGGTGATAACACGGT
*
554567 TCCTACGTGAT-AAGGACGGCTGGTTATCCTAATGT-TGACACGGCTCCTACGTGATGA
64 TCCTACGTGATGAA-GACGGCTGGTTAT-CTAAGGTGTGACACGGCTCCTACGTGATGA
554624 GGAAGTCTGG
Statistics
Matches: 300, Mismatches: 61, Indels: 53
0.72 0.15 0.13
Matches are distributed among these distances:
129 2 0.01
130 34 0.11
131 2 0.01
132 29 0.10
133 30 0.10
134 44 0.15
135 71 0.24
136 53 0.18
137 3 0.01
139 4 0.01
140 2 0.01
141 26 0.09
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (134 bp):
AGGGATGACACGGCTCATACATGATGAAAAACTCTGGCCATCTTAGAAGGGTGATAACACGGTTC
CTACGTGATGAAGACGGCTGGTTATCTAAGGTGTGACACGGCTCCTACGTGATGAAGAGAGCTGG
TCCG
Found at i:554538 original size:130 final size:134
Alignment explanation
Indices: 554377--554623 Score: 355
Period size: 135 Copynumber: 1.9 Consensus size: 134
554367 TATCTATGGT
* *
554377 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATC-TA-AA-GGTGATAACACGGTTCCTACG
1 TGACACGGCTCATACATGATGAAGAAATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
554439 TGATGAA-GACGGCTGGTTAT-CT-ATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCC
66 TGAT-AAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCATACGTGATGAAGAGATCTGGTCC
554501 GGGGGA
129 GGGGGA
* *
554507 TGACACGGTTCATACATGATGAA-AAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCT
1 TGACACGGCTCATACATGATGAAGAAA-TCTGGCCATC-TTA-GAAGGGTGATAACACGGTTCCT
*
554571 ACGTGATAAGGACGGCTGGTTATCCTAATGTTGACACGGCTCCTACGTGATGA
63 ACGTGATAAGGACGGCTGGTTATCCTAATGTTGACACGGCTCATACGTGATGA
554624 GGAAGTCTGG
Statistics
Matches: 103, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
129 2 0.02
130 31 0.30
132 2 0.02
134 4 0.04
135 37 0.36
136 25 0.24
137 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (134 bp):
TGACACGGCTCATACATGATGAAGAAATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
TGATAAGGACGGCTGGTTATCCTAATGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCCGG
GGGA
Found at i:555612 original size:1 final size:1
Alignment explanation
Indices: 555608--555634 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
555598 TTTCCTTCTC
555608 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
555635 AAGTGTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:569395 original size:27 final size:27
Alignment explanation
Indices: 569357--569410 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
569347 CCTTATCTTG
* *
569357 CTTTCGTTTACTTTGTCCTCAATTTAT
1 CTTTCGTTTACTTCGTCCTCAACTTAT
* *
569384 CTTTCTTTTACTTCGTCTTCAACTTAT
1 CTTTCGTTTACTTCGTCCTCAACTTAT
569411 GTCCAAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.24, G:0.06, T:0.56
Consensus pattern (27 bp):
CTTTCGTTTACTTCGTCCTCAACTTAT
Found at i:570128 original size:15 final size:15
Alignment explanation
Indices: 570108--570256 Score: 237
Period size: 15 Copynumber: 10.0 Consensus size: 15
570098 TAATAAGGTT
*
570108 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
*
570123 ATTTATT-TTAAATA
1 ATTTATTATAAAATA
*
570137 ACTTATTATAAAATA
1 ATTTATTATAAAATA
570152 ATTTATTATAAAATA
1 ATTTATTATAAAATA
*
570167 ATTTATTATATAATA
1 ATTTATTATAAAATA
570182 ATTTATTATAAAATA
1 ATTTATTATAAAATA
*
570197 ATTTATTATATAATA
1 ATTTATTATAAAATA
570212 ATTTATTATAAAATA
1 ATTTATTATAAAATA
*
570227 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
570242 ATTTATTATAAAATA
1 ATTTATTATAAAATA
570257 TGGATTGATT
Statistics
Matches: 123, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
14 12 0.10
15 111 0.90
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:570173 original size:30 final size:30
Alignment explanation
Indices: 570108--570300 Score: 237
Period size: 30 Copynumber: 6.3 Consensus size: 30
570098 TAATAAGGTT
* *
570108 ATTTATTTTAAAATAATTTATT-TTAAATA
1 ATTTATTATAAAATAATTTATTATAAAATA
*
570137 ACTTATTATAAAATAATTTATTATAAAATA
1 ATTTATTATAAAATAATTTATTATAAAATA
*
570167 ATTTATTATATAATAATTTATTATAAAATA
1 ATTTATTATAAAATAATTTATTATAAAATA
*
570197 ATTTATTATATAATAATTTATTATAAAATA
1 ATTTATTATAAAATAATTTATTATAAAATA
*
570227 ATTTATTTTAAAATAATTTATTATAAAATATGGA
1 ATTTATTATAAAATAATTTATTAT-AAA-AT--A
* *
570261 TTGATTTATTTTAAAATAATTTATT-TTAAATA
1 ---ATTTATTATAAAATAATTTATTATAAAATA
570293 ATTTATTA
1 ATTTATTA
570301 GTATGGATTG
Statistics
Matches: 147, Mismatches: 9, Indels: 16
0.85 0.05 0.09
Matches are distributed among these distances:
29 27 0.18
30 86 0.59
31 3 0.02
32 3 0.02
34 3 0.02
35 2 0.01
36 1 0.01
37 22 0.15
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (30 bp):
ATTTATTATAAAATAATTTATTATAAAATA
Found at i:570284 original size:15 final size:14
Alignment explanation
Indices: 570264--570299 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
570254 ATATGGATTG
570264 ATTTATTTTAAAATA
1 ATTTATTTT-AAATA
570279 ATTTATTTTAAATA
1 ATTTATTTTAAATA
570293 ATTTATT
1 ATTTATT
570300 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:570317 original size:32 final size:32
Alignment explanation
Indices: 570279--570966 Score: 375
Period size: 32 Copynumber: 23.4 Consensus size: 32
570269 TTTTAAAATA
*
570279 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570311 ATTTATTTT-AA-AA--TA-T-G---A-ATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570333 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570365 ATTTATTTT-AA-AA--TA-T-G---A-ATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570387 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570419 ATTTATTTT-AA-AA--TA-T-G---A-ATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570441 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570473 ATTTA-TTT---TAA---A--A-TATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
*
570495 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570527 ATTTATTTT-AA-AA--TA-T-G----GATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
*
570549 ATTTATTTTAAATAATTTATTAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
** **
570581 ATTTATTTTAAA-ATATGGATT-G-ATTTATT-
1 ATTTATTTTAAATA-ATTTATTAGTATAGATTG
* * * * *
570610 ATTGTAGTTGTATGGATTGATTTATT--T-TA-AATA
1 ATT-TA-TT-T-T-AAATAATTTATTAGTATAGATTG
* * * *
570643 ATTTATTAGTATGAATTGATTTATT--T-TA-AATA
1 ATTTATT--T-T-AAATAATTTATTAGTATAGATTG
* * * *
570675 ATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATT--T-T-AAATAATTTA--TT--AGTATAGATTG
*
570715 ATTTA--TT--AT--TGTAGTT-GTAT-GAATTG
1 ATTTATTTTAAATAATTTA-TTAGTATAG-ATTG
* *
570741 ATTTATTTTAAATAATTTATTAATATAAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570773 ATTTA-TTT---TAA---A--A-TATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570795 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
*
570827 ATTTATTTTAAATAATTTATTTGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
* * *
570859 ATTTATTTTAAAAAAATTATTAGTATAGGTTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
*
570891 ATTTATTTTAAATAATTTATTTGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
*
570923 ATTTATTTTAAAAAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
570955 ATTTATTTTAAA
1 ATTTATTTTAAA
570967 ATATAGATTG
Statistics
Matches: 531, Mismatches: 38, Indels: 174
0.71 0.05 0.23
Matches are distributed among these distances:
22 80 0.15
23 18 0.03
24 8 0.02
25 3 0.01
26 30 0.06
27 8 0.02
28 19 0.04
29 7 0.01
30 20 0.04
31 26 0.05
32 287 0.54
33 5 0.01
34 8 0.02
35 1 0.00
36 1 0.00
38 1 0.00
39 2 0.00
40 7 0.01
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.52
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTG
Found at i:570318 original size:22 final size:22
Alignment explanation
Indices: 570302--570344 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
570292 AATTTATTAG
*
570302 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
570324 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
570345 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:570345 original size:54 final size:54
Alignment explanation
Indices: 570279--570935 Score: 653
Period size: 54 Copynumber: 11.8 Consensus size: 54
570269 TTTTAAAATA
*
570279 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
570333 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
570387 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
570441 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATAT-AGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGA-ATTG
* *
570495 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
* *
570549 ATTTATTTTAAATAATTTATTAATATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
* * * * * * *
570603 ATTTATTATT--GTAGTTGTA-T-GGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATT-TTAAATAATT-TATTAGTATAGATTGA-TTT--AT--TTTA-AAATATGAATTG
*
570661 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-AGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGA-ATTG
* ** *
570715 ATTTA--TT--AT--TGTAGTT-GTAT-GAATTGATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAATAATTTA-TTAGTATAG-ATTGATTTATTTTAAAAT-ATGAATTG
* ** * * * * *
570763 ATATAAATTGATTTATTT-TAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTAT-TAGTATAGATTGATTTATTTT-AA-AA--TA-T-G---A-ATTG
*
570827 ATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAAAAATTATTAGTATAGGTTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT---AAAA-TA-T-G-A-A--TTG
*
570891 ATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
570936 AATTTATTAG
Statistics
Matches: 517, Mismatches: 42, Indels: 81
0.81 0.07 0.13
Matches are distributed among these distances:
47 5 0.01
48 29 0.06
49 2 0.00
50 4 0.01
52 11 0.02
53 10 0.02
54 302 0.58
55 9 0.02
56 1 0.00
57 10 0.02
58 19 0.04
59 10 0.02
60 8 0.02
61 4 0.01
62 3 0.01
64 84 0.16
65 3 0.01
66 3 0.01
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
Found at i:570489 original size:22 final size:22
Alignment explanation
Indices: 570464--570560 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 22
570454 AATTTATTAG
570464 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
570486 TATAGATTGATTTATTTTAAATAA
1 TATAGATTGATTTATTTT-AA-AA
*
570510 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-TAG-ATTGA-T---TTATTTTAAAA
*
570540 TATGGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
570561 TAATTTATTA
Statistics
Matches: 62, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
22 28 0.45
23 2 0.03
24 2 0.03
25 1 0.02
26 6 0.10
27 5 0.08
28 6 0.10
29 1 0.02
30 2 0.03
31 2 0.03
32 7 0.11
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:570648 original size:14 final size:14
Alignment explanation
Indices: 570629--570681 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
570619 GTATGGATTG
570629 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
570643 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
570661 ATTTATTTTAAATA
1 ATTTATTTTAAATA
570675 ATTTATT
1 ATTTATT
570682 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:570666 original size:18 final size:18
Alignment explanation
Indices: 570643--570699 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
570633 ATTTTAAATA
570643 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
570661 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
570675 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
570693 ATTTATT
1 ATTTATT
570700 TTAAAATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:570760 original size:14 final size:15
Alignment explanation
Indices: 570736--570966 Score: 69
Period size: 18 Copynumber: 14.1 Consensus size: 15
570726 TAGTTGTATG
*
570736 AATTGATTTATTTTA
1 AATTAATTTATTTTA
570751 AA-TAATTTATTAATATA
1 AATTAATTTATT--T-TA
*
570768 AATTGATTTATTTTAA
1 AATTAATTTATTTT-A
570784 AATATAGATTGATTTATTTTA
1 AAT-T--A---ATTTATTTTA
570805 AA-TAATTTATTAGTATA
1 AATTAATTTATT--T-TA
* *
570822 GATTGATTTATTTTA
1 AATTAATTTATTTTA
570837 AA-TAATTTATTTGTA
1 AATTAATTTATTT-TA
*
570852 TAGATTGATTTATTTTA
1 -A-ATTAATTTATTTTA
* *
570869 AA-AAAATTATTAGTATA
1 AATTAATTTATT--T-TA
** *
570886 GGTTGATTTATTTTA
1 AATTAATTTATTTTA
570901 AA-TAATTTATTTGTA
1 AATTAATTTATTT-TA
*
570916 TAGATTGATTTATTTTA
1 -A-ATTAATTTATTTTA
*
570933 AA-AAATTTATTAGTATA
1 AATTAATTTATT--T-TA
* *
570950 GATTGATTTATTTTA
1 AATTAATTTATTTTA
570965 AA
1 AA
570967 ATATAGATTG
Statistics
Matches: 159, Mismatches: 26, Indels: 62
0.64 0.11 0.25
Matches are distributed among these distances:
14 46 0.29
15 17 0.11
16 16 0.10
17 20 0.13
18 47 0.30
19 1 0.01
21 3 0.02
22 9 0.06
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (15 bp):
AATTAATTTATTTTA
Found at i:570787 original size:22 final size:22
Alignment explanation
Indices: 570762--570806 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
570752 ATAATTTATT
570762 AATATAAATTGATTTATTTTAA
1 AATATAAATTGATTTATTTTAA
*
570784 AATATAGATTGATTTATTTTAA
1 AATATAAATTGATTTATTTTAA
570806 A
1 A
570807 TAATTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (22 bp):
AATATAAATTGATTTATTTTAA
Found at i:570971 original size:22 final size:22
Alignment explanation
Indices: 570946--570988 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
570936 AATTTATTAG
570946 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
570968 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
570989 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:571048 original size:31 final size:31
Alignment explanation
Indices: 571013--571071 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
571003 AGTTGTATGG
* *
571013 ATTATTTAAATTTCAATATTGTAAAACTAAA
1 ATTATTTAAATATCAATATTGCAAAACTAAA
*
571044 ATTATTTAAATATCAGTATTGCAAAACT
1 ATTATTTAAATATCAATATTGCAAAACT
571072 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATATCAATATTGCAAAACTAAA
Found at i:575127 original size:32 final size:32
Alignment explanation
Indices: 575091--575153 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
575081 TCTATAGTAC
575091 ATAATGCAATATGTTTTGTAAGTAAAACAATA
1 ATAATGCAATATGTTTTGTAAGTAAAACAATA
575123 ATAATGCAATATGTTTTGTAAGTAAAACAAT
1 ATAATGCAATATGTTTTGTAAGTAAAACAAT
575154 GTGATTCGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (32 bp):
ATAATGCAATATGTTTTGTAAGTAAAACAATA
Found at i:578510 original size:27 final size:28
Alignment explanation
Indices: 578476--578540 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
578466 AATATAAGAG
578476 TTTA-TTTTAGTTATAGAAAA-T-ATTTT
1 TTTATTTTTAGTTATA-AAAAGTAATTTT
* *
578502 TTTATTTTTATTTTTAAAAAGTAATTTT
1 TTTATTTTTAGTTATAAAAAGTAATTTT
578530 TTTAATTTTTA
1 TTT-ATTTTTA
578541 AAATCTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 8 0.24
27 10 0.30
28 8 0.24
29 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTATTTTTAGTTATAAAAAGTAATTTT
Found at i:578592 original size:76 final size:78
Alignment explanation
Indices: 578471--578618 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 78
578461 GGAGAAATAT
* * * *
578471 AAGAGTTTATTTTAGTTATAGAAAATATTTTTTTATTTTTATTTTTAAAAAGTAATTTTTTTAAT
1 AAGAGTTTATTTGAGTTATAGAAAATATTTTTCTATTTTTATTTTTAAAAAAT-ATTTTTCTAAT
*
578536 TTTTAAAATCTATA
65 TTTCAAAATCTATA
*
578550 AAGA-TTTATTTGA-TTCTAGAAAATA-TTTTCTATTTTTATTTTTAAAAAATATTTTTCTAATT
1 AAGAGTTTATTTGAGTTATAGAAAATATTTTTCTATTTTTATTTTTAAAAAATATTTTTCTAATT
578612 TTCAAAA
66 TTCAAAA
578619 CATACAATGC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
75 17 0.27
76 23 0.37
77 11 0.17
78 8 0.13
79 4 0.06
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.54
Consensus pattern (78 bp):
AAGAGTTTATTTGAGTTATAGAAAATATTTTTCTATTTTTATTTTTAAAAAATATTTTTCTAATT
TTCAAAATCTATA
Found at i:579362 original size:14 final size:14
Alignment explanation
Indices: 579345--579372 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
579335 TTTTTTAATT
579345 TAAAAATATAAATA
1 TAAAAATATAAATA
579359 TAAAAATATAAATA
1 TAAAAATATAAATA
579373 ATTATTAAGA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAAATATAAATA
Found at i:579486 original size:3 final size:3
Alignment explanation
Indices: 579478--579521 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
579468 CAAGGATCAC
579478 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
579522 GCAAAAGTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:580078 original size:78 final size:79
Alignment explanation
Indices: 579939--580098 Score: 209
Period size: 78 Copynumber: 2.0 Consensus size: 79
579929 AAATAATAAT
* *
579939 AATTTTTAATATTTCTGATAAAACATTATATAAAATATTATTTTTTATACCGAAAATATTAATAG
1 AATTTTTAACATTTCTGATAAAACATTATATAAAACATTATTTTTTATACCGAAAATATTAATAG
* * *
580004 TGGGTGCTACTTAA
66 TAGGTACTACCTAA
* *
580018 AATTTTTAACATTTCCTG-TAAAACGTTACT-T-AAACATTATTTTTTATACTGAAAATATTAAT
1 AATTTTTAACATTT-CTGATAAAACATTA-TATAAAACATTATTTTTTATACCGAAAATATTAAT
*
580080 ATTAGGTACTACCTAA
64 AGTAGGTACTACCTAA
580096 AAT
1 AAT
580099 ATTATTTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
78 44 0.62
79 23 0.32
80 4 0.06
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (79 bp):
AATTTTTAACATTTCTGATAAAACATTATATAAAACATTATTTTTTATACCGAAAATATTAATAG
TAGGTACTACCTAA
Found at i:596080 original size:6 final size:6
Alignment explanation
Indices: 596069--596110 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
596059 TATAAGGACT
596069 GAATTA GAATTA GAATTA GAATTA GAATTA GAATTA GAATTA
1 GAATTA GAATTA GAATTA GAATTA GAATTA GAATTA GAATTA
596111 AAATAAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
GAATTA
Found at i:601574 original size:57 final size:57
Alignment explanation
Indices: 601503--601616 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
601493 TTAGCAAAGG
* *
601503 TGATTAAACAAGGAATCTGATTATCTTTGATTTGTCTAGGTCCTAAAACAAAAGCTT
1 TGATTAAACAAGGAATCTGATCATCTTTGATTTGTCTAGATCCTAAAACAAAAGCTT
*
601560 TGATTAAACAAGGAATCTGGTCATCTTTGATTTGTCTAGATCCTAAAACAAAAGCTT
1 TGATTAAACAAGGAATCTGATCATCTTTGATTTGTCTAGATCCTAAAACAAAAGCTT
601617 GGTTGCACAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (57 bp):
TGATTAAACAAGGAATCTGATCATCTTTGATTTGTCTAGATCCTAAAACAAAAGCTT
Found at i:604840 original size:34 final size:35
Alignment explanation
Indices: 604768--604841 Score: 118
Period size: 34 Copynumber: 2.2 Consensus size: 35
604758 AACTGAGAAA
604768 ATTT-AAGAAAATTTAAATTTAAATTTTCCATCTT
1 ATTTAAAGAAAATTTAAATTTAAATTTTCCATCTT
*
604802 -TTTAAAGAAAATTTAAATTTAAATTTT-CATTTT
1 ATTTAAAGAAAATTTAAATTTAAATTTTCCATCTT
604835 ATTTAAA
1 ATTTAAA
604842 TAAATTTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
33 8 0.22
34 29 0.78
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (35 bp):
ATTTAAAGAAAATTTAAATTTAAATTTTCCATCTT
Found at i:604847 original size:21 final size:22
Alignment explanation
Indices: 604812--604855 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
604802 TTTAAAGAAA
604812 ATTTAAATTTAAATTTTCATTTT
1 ATTTAAA-TTAAATTTTCATTTT
604835 ATTTAAA-TAAATTTTCATTTT
1 ATTTAAATTAAATTTTCATTTT
604856 CTATTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.67
23 7 0.33
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTAAATTAAATTTTCATTTT
Found at i:606486 original size:13 final size:13
Alignment explanation
Indices: 606468--606498 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
606458 GTAACAATAG
606468 AAAATGAGAAGGA
1 AAAATGAGAAGGA
606481 AAAATGAGAAGGA
1 AAAATGAGAAGGA
606494 AAAAT
1 AAAAT
606499 TCAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.10
Consensus pattern (13 bp):
AAAATGAGAAGGA
Found at i:608228 original size:32 final size:28
Alignment explanation
Indices: 608191--608269 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 28
608181 AGTATTTTTT
*
608191 TAAATAGTTATTATATTTTATATATAATTATA
1 TAAATA-TTATTAT-TTTTA-AAATAA-TATA
*
608223 TAAATATTATT-TTTATTAAAATAATATT
1 TAAATATTATTATTT-TTAAAATAATATA
608251 TAAATAATTATTATTTTTA
1 TAAAT-ATTATTATTTTTA
608270 GAATTATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
28 8 0.19
29 16 0.38
30 7 0.17
31 5 0.12
32 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
TAAATATTATTATTTTTAAAATAATATA
Found at i:608238 original size:17 final size:17
Alignment explanation
Indices: 608218--608269 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
608208 TTATATATAA
608218 TTATATAAATATTATTT
1 TTATATAAATATTATTT
* *
608235 TTAT-TAAA-ATAATAT
1 TTATATAAATATTATTT
* *
608250 TTAAATAATTATTATTT
1 TTATATAAATATTATTT
608267 TTA
1 TTA
608270 GAATTATTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 8 0.30
16 7 0.26
17 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATAAATATTATTT
Found at i:608279 original size:26 final size:25
Alignment explanation
Indices: 608199--608289 Score: 69
Period size: 28 Copynumber: 3.4 Consensus size: 25
608189 TTTAAATAGT
*
608199 TATTATATTTTATATATAATTATATAAA
1 TATTAT-TTTTAT-TAAAATTAT-TAAA
608227 TATTATTTTTATTAAAATAATATTTAAA
1 TATTATTTTTATTAAAAT--TA-TTAAA
* *
608255 TAATTATTATTT-TTAGAATTATTAAT
1 T-ATTATT-TTTATTAAAATTATTAAA
608281 TATT-TTTTT
1 TATTATTTTT
608290 GCTAATTATA
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
23 3 0.05
24 2 0.04
25 3 0.05
26 10 0.18
27 8 0.15
28 13 0.24
29 13 0.24
30 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
TATTATTTTTATTAAAATTATTAAA
Found at i:608438 original size:17 final size:16
Alignment explanation
Indices: 608416--608469 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
608406 TAATGTTAAT
608416 ATTTAAATTTATTTTTA
1 ATTTAAA-TTATTTTTA
* *
608433 ATTTAAAGTTATTATGA
1 ATTTAAA-TTATTTTTA
* *
608450 ATTTATATTAATTTTA
1 ATTTAAATTATTTTTA
608466 ATTT
1 ATTT
608470 TTTATAATGT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTTAAATTATTTTTA
Found at i:617978 original size:2 final size:2
Alignment explanation
Indices: 617971--618066 Score: 86
Period size: 2 Copynumber: 53.0 Consensus size: 2
617961 ACGCCCCGAT
*
617971 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
618013 T- TT TA TA T- TA -A T- TA TA TA TA TA -A TA T- TT TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
618048 TT TA TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
618067 AAATATTTTC
Statistics
Matches: 79, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
1 10 0.13
2 69 0.87
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:618067 original size:32 final size:35
Alignment explanation
Indices: 617989--618072 Score: 143
Period size: 34 Copynumber: 2.4 Consensus size: 35
617979 TATATATATA
617989 TATATATATATATATATTTATATATTTTATATTAAT
1 TATATATATA-ATATATTTATATATTTTATATTAAT
618025 TATATATATAATAT-TTTATATATTTTATATTAAT
1 TATATATATAATATATTTATATATTTTATATTAAT
*
618059 TATATATAAAATAT
1 TATATATATAATAT
618073 TTTCGGGTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
34 33 0.70
35 4 0.09
36 10 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
TATATATATAATATATTTATATATTTTATATTAAT
Found at i:624180 original size:38 final size:39
Alignment explanation
Indices: 624129--624217 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 39
624119 ATTTAAGGGG
* * *
624129 GAATTTTATAGTCTCTTGGGAGTTA-AATGTTTTATTGT
1 GAATTTAAGAGTCTCTTGGGAGTTAGAATGTTTTATTAT
*
624167 GAATTTAAGAGTCTCTTGGGAGTTAGAGTGTTTTATTAT
1 GAATTTAAGAGTCTCTTGGGAGTTAGAATGTTTTATTAT
624206 GAATTTAAGAGT
1 GAATTTAAGAGT
624218 TTTTGGAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 23 0.50
39 23 0.50
ACGTcount: A:0.27, C:0.04, G:0.24, T:0.45
Consensus pattern (39 bp):
GAATTTAAGAGTCTCTTGGGAGTTAGAATGTTTTATTAT
Found at i:625099 original size:22 final size:22
Alignment explanation
Indices: 625073--625173 Score: 60
Period size: 25 Copynumber: 4.2 Consensus size: 22
625063 TATTTTTAAT
625073 TATATTTTATTTATTTAT-TTA
1 TATATTTTATTTATTTATATTA
*
625094 CTATATTCCTTTTTTATTTATATTA
1 -TATATT--TTATTTATTTATATTA
* *
625119 TATTATTTTTATTATATATATCTTA
1 TA-TA-TTTTATT-TATTTATATTA
* *
625144 TATCATTATGTATATATATATATATA
1 TAT-ATT-T-TATTTATTTATAT-TA
625170 TATA
1 TATA
625174 GATGTATTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
22 6 0.10
24 20 0.32
25 27 0.43
26 10 0.16
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (22 bp):
TATATTTTATTTATTTATATTA
Found at i:625126 original size:14 final size:14
Alignment explanation
Indices: 625107--625146 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
625097 TATTCCTTTT
625107 TTATTTATATTATA
1 TTATTTATATTATA
*
625121 TTATTTTTATTATA
1 TTATTTATATTATA
625135 TATATCTTATAT
1 T-TAT-TTATAT
625147 CATTATGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:625144 original size:20 final size:20
Alignment explanation
Indices: 625057--625137 Score: 62
Period size: 20 Copynumber: 4.0 Consensus size: 20
625047 TCATCCCCTA
*
625057 TATATATATTTTTAATTATAT
1 TATAT-TATTTTTATTTATAT
* *
625078 TTTATT-TATTTATTTACTA-
1 TATATTATTTTTATTTA-TAT
625097 TAT-TCCT-TTTTTATTTATAT
1 TATAT--TATTTTTATTTATAT
625117 TATATTATTTTTATTATATAT
1 TATATTATTTTTATT-TATAT
625138 ATCTTATATC
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
18 1 0.02
19 13 0.27
20 24 0.50
21 10 0.21
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TATATTATTTTTATTTATAT
Found at i:625463 original size:18 final size:17
Alignment explanation
Indices: 625431--625475 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
625421 TGTACACATT
625431 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
625448 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
625466 ATTTTTTTAC
1 ATTTTTTTAC
625476 TCCATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:625473 original size:17 final size:17
Alignment explanation
Indices: 625429--625475 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
625419 TATGTACACA
625429 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
625446 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
625464 TTATTTTTTTAC
1 TTATTTTTTTAC
625476 TCCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:630100 original size:18 final size:19
Alignment explanation
Indices: 630066--630102 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
630056 GAAAAAAGAG
*
630066 AAAAAAGCAAAGAGAAAAT
1 AAAAAAACAAAGAGAAAAT
630085 AAAAAAACAAAG-GAAAAT
1 AAAAAAACAAAGAGAAAAT
630103 TGAAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (19 bp):
AAAAAAACAAAGAGAAAAT
Found at i:630252 original size:69 final size:69
Alignment explanation
Indices: 630174--630311 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
630164 GATTCAAACT
630174 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTAAATCACTTCACTCAAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTAAATCACTTCACTCAAAGATCATAGAGCA
630239 TCAA
66 TCAA
* * *
630243 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTTACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTAAATCACTTCACTCAAAGATCATAGAGCA
630308 TCAA
66 TCAA
630312 GAGAGACACA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTTCGAATCACTAAATCACTTCACTCAAAGATCATAGAGCA
TCAA
Found at i:631320 original size:33 final size:33
Alignment explanation
Indices: 631246--631359 Score: 151
Period size: 32 Copynumber: 3.5 Consensus size: 33
631236 TGAGGGCATC
631246 TTTGAAGATTCAACATCAAATGTTGGGGCATTTT
1 TTTG-AGATTCAACATCAAATGTTGGGGCATTTT
*
631280 TTT-AGATTTAACATCAAATGTTGGGGCATTTT
1 TTTGAGATTCAACATCAAATGTTGGGGCATTTT
* * *
631312 TTTGAGATTCAACATCGAATATTGGGGCATCTT
1 TTTGAGATTCAACATCAAATGTTGGGGCATTTT
**
631345 TGGGA-ATTCAACATC
1 TTTGAGATTCAACATC
631360 CTGATGCAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 41 0.57
33 28 0.39
34 3 0.04
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (33 bp):
TTTGAGATTCAACATCAAATGTTGGGGCATTTT
Found at i:632062 original size:106 final size:106
Alignment explanation
Indices: 631937--632146 Score: 375
Period size: 106 Copynumber: 2.0 Consensus size: 106
631927 ATATCGTGCC
* *
631937 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAAAATTTCCC
*
632002 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
632043 ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAAAATTTCCC
1 ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAAAATTTCCC
*
632108 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
632147 TGTAACATCC
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAAAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:633373 original size:16 final size:17
Alignment explanation
Indices: 633339--633378 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
633329 TTATATGAAA
*
633339 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
633356 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
633372 TGATATG
1 TGATATG
633379 CCATATGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:633995 original size:23 final size:23
Alignment explanation
Indices: 633949--633997 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
633939 TATGGAACTA
*
633949 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
*
633972 CGGTGCATTTCTACGCGGTC-CTT
1 CGGTGCAATTCTACGCGG-CACTT
633995 CGG
1 CGG
633998 GACAAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.31
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTT
Found at i:636330 original size:20 final size:19
Alignment explanation
Indices: 636275--636344 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
636265 TATATATATA
*
636275 TTTTTAATTATATT-TTAT
1 TTTTTATTTATATTATTAT
*
636293 TTATTTATTTACTA-TATTCCT
1 TT-TTTATTTA-TATTATT-AT
636314 TTTTTATTTATATTATT-T
1 TTTTTATTTATATTATTAT
* *
636332 TTATTATATATAT
1 TTTTTATTTATAT
636345 CTTATATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 14 0.33
19 10 0.23
20 16 0.37
21 3 0.07
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTATTTATATTATTAT
Found at i:636343 original size:2 final size:2
Alignment explanation
Indices: 636336--636389 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
636326 TTATTTTTAT
* *
636336 TA TA TA TA TC T- TA TA TA -A T- TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
636375 TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA T
636390 GTATTAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:636390 original size:8 final size:8
Alignment explanation
Indices: 636355--636393 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
636345 CTTATATAAT
636355 TATGTATA
1 TATGTATA
*
636363 TATATATA
1 TATGTATA
*
636371 TATATATA
1 TATGTATA
636379 TATGTATA
1 TATGTATA
636387 TATGTAT
1 TATGTAT
636394 TAATTTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (8 bp):
TATGTATA
Found at i:637688 original size:54 final size:53
Alignment explanation
Indices: 637603--637706 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 53
637593 TTTGATGTTT
*
637603 ATAAAAACACATTTTTTGCCAAAATTATCAACAATCATAAAAAAAAAATCAAC
1 ATAAAAACACATTTTTTGACAAAATTATCAACAATCATAAAAAAAAAATCAAC
* * *
637656 ATAAAAACACATTTTTTTAGAC-AAATTATCAACATTCATAATAAACAAATC
1 ATAAAAACACA-TTTTTT-GACAAAATTATCAACAATCATAAAAAAAAAATC
637707 TACTAACATG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
53 11 0.24
54 32 0.71
55 2 0.04
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (53 bp):
ATAAAAACACATTTTTTGACAAAATTATCAACAATCATAAAAAAAAAATCAAC
Found at i:639290 original size:18 final size:18
Alignment explanation
Indices: 639252--639328 Score: 109
Period size: 18 Copynumber: 4.2 Consensus size: 18
639242 AAAACATAAC
639252 AAAGTATTTCTAATCATCAA
1 AAAGTATTTCTAATC--CAA
639272 AAAGTATTTCTAATCCAA
1 AAAGTATTTCTAATCCAA
* *
639290 AAACTTTTTCTAATCCAA
1 AAAGTATTTCTAATCCAA
*
639308 AGAGTATTTCTAATCCAA
1 AAAGTATTTCTAATCCAA
639326 AAA
1 AAA
639329 AACACATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
18 36 0.71
20 15 0.29
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (18 bp):
AAAGTATTTCTAATCCAA
Found at i:640840 original size:18 final size:17
Alignment explanation
Indices: 640798--640858 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 17
640788 TCTCTACGGT
640798 GGATGAATCGACCGAATGA
1 GGATGAA-CGACCGAA-GA
640817 GG-TGAACGACCGAAGAA
1 GGATGAACGACCGAAG-A
640834 GGATGAACGACCGAAGGA
1 GGATGAACGACCGAA-GA
640852 GGATGAA
1 GGATGAA
640859 TCGATTGCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.03
17 11 0.28
18 24 0.62
19 3 0.08
ACGTcount: A:0.39, C:0.15, G:0.36, T:0.10
Consensus pattern (17 bp):
GGATGAACGACCGAAGA
Found at i:645095 original size:35 final size:35
Alignment explanation
Indices: 645055--645128 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
645045 GATTTCGGGA
*
645055 TTTTGCTATTTTTGGC-AAATTCGAATAAATACGAT
1 TTTTGCTA-TTTTGGCAAAATTCGAATAAAGACGAT
645090 TTTTGCTATTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTGGCAAAATTCGAATAAAGACGAT
645125 TTTT
1 TTTT
645129 TAGCTATAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
34 7 0.19
35 30 0.81
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (35 bp):
TTTTGCTATTTTGGCAAAATTCGAATAAAGACGAT
Found at i:647185 original size:31 final size:31
Alignment explanation
Indices: 647150--647243 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 31
647140 CAAAAGCTTG
*
647150 GGGATTAATTTAGAAAGAGGGTCATAGTTTA
1 GGGATTAATTTAGAAAGAGTGTCATAGTTTA
* * * * * *
647181 GGGATGAAATTAG-AA-TGTTTAAAAGTTTA
1 GGGATTAATTTAGAAAGAGTGTCATAGTTTA
* * *
647210 AGGACTAATTTAGAATGAGTGTCATAGTTTA
1 GGGATTAATTTAGAAAGAGTGTCATAGTTTA
647241 GGG
1 GGG
647244 GTCGAATTGA
Statistics
Matches: 44, Mismatches: 17, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
29 18 0.41
30 3 0.07
31 23 0.52
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (31 bp):
GGGATTAATTTAGAAAGAGTGTCATAGTTTA
Found at i:647220 original size:60 final size:60
Alignment explanation
Indices: 647128--647304 Score: 171
Period size: 60 Copynumber: 3.0 Consensus size: 60
647118 ATGGGTATGA
* * ** * *
647128 AATTGGAATATTCAAAAGCTTGGGGATTAATTTAGAAAGAGGGTCATAGTTTAGGGAT-G
1 AATTGAAATATTCAAAAGTTTAAGAACTAATTTAGAAAGAGGGTCATAGTTTAGGGATCG
* * * * * *
647187 AAATT-AGAATGTTTAAAAGTTTAAGGACTAATTTAGAATGAGTGTCATAGTTTAGGGGTCG
1 -AATTGA-AATATTCAAAAGTTTAAGAACTAATTTAGAAAGAGGGTCATAGTTTAGGGATCG
* * *
647248 AATTGAAATATTCAAAAGTTTAAGAACTAATTTA-AAATGAGGCTTATAGTTTGGGGA
1 AATTGAAATATTCAAAAGTTTAAGAACTAATTTAGAAA-GAGGGTCATAGTTTAGGGA
647305 CATATGATGT
Statistics
Matches: 94, Mismatches: 19, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
59 2 0.02
60 90 0.96
61 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (60 bp):
AATTGAAATATTCAAAAGTTTAAGAACTAATTTAGAAAGAGGGTCATAGTTTAGGGATCG
Found at i:648293 original size:46 final size:46
Alignment explanation
Indices: 648225--648335 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
648215 AATAAGGTTG
* *
648225 TGTTTGCTTTCTTT-TATTTCTTTTTTAAGCAGTTCTTGTTTAGTTCA
1 TGTTTG-TTTCTTTAT-TTTCTTTTTGAAGCAGTTCGTGTTTAGTTCA
648272 TGTTTGTTTCTTTATTTTCTTTTTGAAGCAGTTCGTGTTTAGTTCA
1 TGTTTGTTTCTTTATTTTCTTTTTGAAGCAGTTCGTGTTTAGTTCA
648318 TGTTTGTTTCTTTATTTT
1 TGTTTGTTTCTTTATTTT
648336 TTAAATTGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
46 54 0.89
47 7 0.11
ACGTcount: A:0.12, C:0.11, G:0.14, T:0.63
Consensus pattern (46 bp):
TGTTTGTTTCTTTATTTTCTTTTTGAAGCAGTTCGTGTTTAGTTCA
Found at i:655040 original size:26 final size:28
Alignment explanation
Indices: 655005--655056 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
654995 GTTAGGGAGT
*
655005 AATTTCTAAAATTTT-AGAG-ATAAACG
1 AATTTATAAAATTTTAAGAGAATAAACG
*
655031 AATTTATAAAGTTTTAAGAGAATAAA
1 AATTTATAAAATTTTAAGAGAATAAA
655057 AACATATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 4 0.18
28 5 0.23
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.35
Consensus pattern (28 bp):
AATTTATAAAATTTTAAGAGAATAAACG
Found at i:660346 original size:12 final size:12
Alignment explanation
Indices: 660331--660385 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
660321 GTTATTTAAA
660331 CGGGTATTGGGC
1 CGGGTATTGGGC
* *
660343 CGGGTATTGAGT
1 CGGGTATTGGGC
*
660355 CGGGTATTGGGT
1 CGGGTATTGGGC
* *
660367 CGGGAATCGGGC
1 CGGGTATTGGGC
660379 CGGGTAT
1 CGGGTAT
660386 ATATATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:660447 original size:24 final size:25
Alignment explanation
Indices: 660383--660447 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
660373 TCGGGCCGGG
660383 TATATATATATATATATTTAAATTAAA
1 TATATAT-TATAT-TATTTAAATTAAA
*
660410 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
660434 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
660448 ATATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.56
25 2 0.06
26 1 0.03
27 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:660493 original size:12 final size:13
Alignment explanation
Indices: 660477--660525 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
660467 TTTAATATTT
*
660477 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
**
660489 ATCGGGATGGGTA
1 ATCGGGGCGGGTA
660502 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
660515 ATCGGGGCGGG
1 ATCGGGGCGGG
660526 GATTACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 10 0.31
13 22 0.69
ACGTcount: A:0.14, C:0.14, G:0.53, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:661760 original size:42 final size:42
Alignment explanation
Indices: 661713--661818 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 42
661703 AAATTTTGTA
* * * *
661713 TTTGTTTTATGTAATTTGTTTTTTGAAAAATATTTTTTCATG
1 TTTGTTTCACGTAATTCGTTTTTCGAAAAATATTTTTTCATG
*
661755 TTTGTTTCACGTAATTCGTTTTTCGAAAAATATTTTTTCGTG
1 TTTGTTTCACGTAATTCGTTTTTCGAAAAATATTTTTTCATG
*
661797 TTTGTTTCACGTAATTCATTTT
1 TTTGTTTCACGTAATTCGTTTT
661819 CTAGAATGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.22, C:0.08, G:0.12, T:0.58
Consensus pattern (42 bp):
TTTGTTTCACGTAATTCGTTTTTCGAAAAATATTTTTTCATG
Found at i:662022 original size:14 final size:15
Alignment explanation
Indices: 661996--662026 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
661986 CATTTTCATC
661996 AAAATATTATTTATT
1 AAAATATTATTTATT
662011 AAAATA-TATTTATT
1 AAAATATTATTTATT
662025 AA
1 AA
662027 TATTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATATTATTTATT
Found at i:662051 original size:22 final size:24
Alignment explanation
Indices: 662003--662066 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 24
661993 ATCAAAATAT
*
662003 TATTTATTAA-AATATATTTATTAA
1 TATTTA-TAATAATATATATATTAA
662027 TATTTATAATAATATA-ATATT-A
1 TATTTATAATAATATATATATTAA
* *
662049 TATTTTTAATATTATATA
1 TATTTATAATAATATATA
662067 AAATAATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 15 0.43
23 8 0.23
24 12 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTTATAATAATATATATATTAA
Found at i:662150 original size:28 final size:29
Alignment explanation
Indices: 662119--662181 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
662109 ATTTTTATTT
*
662119 TAATATATAATATTTTTTATATATTT-AA
1 TAATATATAATATTATTTATATATTTAAA
662147 TAATGA-ATAATATTATTTATATATTTAAA
1 TAAT-ATATAATATTATTTATATATTTAAA
662176 TAATAT
1 TAATAT
662182 TTTAATAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TAATATATAATATTATTTATATATTTAAA
Found at i:662210 original size:23 final size:23
Alignment explanation
Indices: 662184--662228 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
662174 AATAATATTT
662184 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
662207 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
662229 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:662352 original size:18 final size:19
Alignment explanation
Indices: 662321--662357 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
662311 ATATAAAATT
662321 ATAAAAATAATATTTAATA
1 ATAAAAATAATATTTAATA
*
662340 ATAAAAA-ATTATTTAATA
1 ATAAAAATAATATTTAATA
662358 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAAATAATATTTAATA
Found at i:662528 original size:15 final size:15
Alignment explanation
Indices: 662508--662547 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
662498 AGATGTTTTC
*
662508 CAGTAATTCAAATTT
1 CAGTAATTCAAATTG
662523 CAGTAATTCAAATTG
1 CAGTAATTCAAATTG
662538 CAGTAATTCA
1 CAGTAATTCA
662548 TTTTCCGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (15 bp):
CAGTAATTCAAATTG
Found at i:664101 original size:227 final size:227
Alignment explanation
Indices: 663663--664109 Score: 756
Period size: 227 Copynumber: 2.0 Consensus size: 227
663653 GTAAATTATC
* * *
663663 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
663728 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
663793 TGTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAAAACATAAAACACTATTAAAAAAATTG
663858 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
663891 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
663956 TTAATA-TGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
664019 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGG-AAAACATAAAACACTATTAAATAAAT
130 TTGTGTAAATGAAATTATTAAATTAATA-TGTAGGTGGAAAAACATAAAACACTATTAAAAAAAT
664083 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
664110 GCAGTTTTAA
Statistics
Matches: 207, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
226 4 0.02
227 90 0.43
228 83 0.40
229 30 0.14
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:664362 original size:20 final size:19
Alignment explanation
Indices: 664339--664385 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
664329 CGATATAACA
*
664339 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
664359 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
664379 GGTAAAA
1 GGTAAAA
664386 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:666712 original size:33 final size:33
Alignment explanation
Indices: 666670--666735 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
666660 AAATAGATGG
*
666670 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
666703 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
666736 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:668573 original size:19 final size:19
Alignment explanation
Indices: 668529--668572 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
668519 AATGTCGAGT
668529 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
668548 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
668567 T-ATTTT
1 TAATTTT
668573 TTATGTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:669057 original size:197 final size:198
Alignment explanation
Indices: 668654--670250 Score: 2836
Period size: 195 Copynumber: 8.1 Consensus size: 198
668644 TTAAGGGTCA
* * *
668654 TGTCGATACTAATATAGTTTGTGTCGATTTTTTTTTCCAGAATGAATT-AAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
668718 ATAAAG-GTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
668781 AATATGT-ATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
668845 ATG
196 ATG
*
668848 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
668913 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA-CGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
* *
668977 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATG
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
669042 ATG
196 ATG
669045 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
*
669110 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
669175 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
669240 AATG
195 AATG
*
669244 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
669309 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
669373 AATATGTAATTTTTTAATCTAA-CGGTACAATTATACCGG-TTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
669436 ATG
196 ATG
* *
669439 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGAATGAATTAAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
669504 ATAAA--GTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
669567 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
669632 AATG
195 AATG
*
669636 TGTCGACACTAATATAG-TTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
669700 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
669765 AATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
669829 ATG
196 ATG
*
669832 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
*
669897 CATAAAGTGTCGAT--ATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
669959 TAATATGTAATTTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
670023 AATG
195 AATG
* *
670027 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGAATGAATTAAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
*
670092 ATAAAGTGTCGATCC--ATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
* * *
670155 AATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTT-TGAGAGAATATGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
670219 ATG
196 ATG
*
670222 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
670251 CTAATTAAAT
Statistics
Matches: 1358, Mismatches: 26, Indels: 37
0.96 0.02 0.03
Matches are distributed among these distances:
193 14 0.01
194 91 0.07
195 434 0.32
196 251 0.18
197 274 0.20
198 172 0.13
199 122 0.09
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATG
Found at i:669744 original size:392 final size:396
Alignment explanation
Indices: 668654--670250 Score: 2890
Period size: 392 Copynumber: 4.1 Consensus size: 396
668644 TTAAGGGTCA
* * *
668654 TGTCGATACTAATATAGTTTGTGTCGAT-TTTTTTTTCCAGAATGAATT-AAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
668717 AATAAAGGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATGT
66 CATAAAGGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
668781 AATATGT-ATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
668845 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCA
196 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCA
668910 TCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA-CGAACCCAAAAGTATAA
261 TCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
668974 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
326 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
*
669039 ATGATG
391 ATAATG
669045 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
669110 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAG-GTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
669175 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
669240 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
195 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
669305 ATCAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
260 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
*
669369 ATGTAATATGTAATTTTTTAATCTAA-CGGTACAATTATACCGG-TTTATGAGAGAATAAGTCTA
325 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
669432 AATAATG
390 AATAATG
669439 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
669503 CATAAA-GTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
669567 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
669632 AATGTGTCGACACTAATATAG-TTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
195 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
669696 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
260 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
669761 ATGTAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
325 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
669825 AATAATG
390 AATAATG
*
669832 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
669897 CATAAAGTGTCGAT--ATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAG-GTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
669959 TAATATGTAATTTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
670023 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGAATGAATTAAAAACAAGGTGC
195 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
* * *
670088 ACCCATAAAGTGTCGATCC--ATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
260 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
* *
670151 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTT-TGAGAGAATATGTCTA
325 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
670215 AATAATG
390 AATAATG
*
670222 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
670251 CTAATTAAAT
Statistics
Matches: 1175, Mismatches: 16, Indels: 31
0.96 0.01 0.03
Matches are distributed among these distances:
390 111 0.09
391 205 0.17
392 345 0.29
393 117 0.10
394 146 0.12
395 58 0.05
396 193 0.16
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (396 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCA
TCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
ATAATG
Found at i:671727 original size:12 final size:12
Alignment explanation
Indices: 671710--671801 Score: 76
Period size: 12 Copynumber: 7.4 Consensus size: 12
671700 GGTCGCAGAA
*
671710 GATGAAGCTGAC
1 GATGAAGATGAC
671722 GATGAAGATGAC
1 GATGAAGATGAC
671734 GATGATGATGATGAC
1 GATGA--A-GATGAC
* *
671749 GATGAAGCTGGC
1 GATGAAGATGAC
*
671761 GATGAAGATGAT
1 GATGAAGATGAC
* * *
671773 GACGATGATGAT
1 GATGAAGATGAC
* *
671785 GATGATGATGAA
1 GATGAAGATGAC
671797 GATGA
1 GATGA
671802 TGATCCAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
12 54 0.81
13 1 0.01
14 1 0.01
15 11 0.16
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:671731 original size:6 final size:6
Alignment explanation
Indices: 671707--671801 Score: 55
Period size: 6 Copynumber: 15.3 Consensus size: 6
671697 ATCGGTCGCA
* * * * *
671707 GAAGAT GAAGCT GACGAT GAAGAT GACGATGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GAAGAT
** * * * * *
671758 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
671802 TGATCCAAAA
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
6 63 0.91
8 1 0.01
9 5 0.07
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:671746 original size:15 final size:15
Alignment explanation
Indices: 671722--671804 Score: 91
Period size: 15 Copynumber: 5.7 Consensus size: 15
671712 TGAAGCTGAC
*
671722 GATGAAGATGACGAT
1 GATGATGATGACGAT
671737 GATGATGATGACGAT
1 GATGATGATGACGAT
* *
671752 GA--A-GCTGGCGAT
1 GATGATGATGACGAT
*
671764 GAAGATGATGACGAT
1 GATGATGATGACGAT
*
671779 GATGATGATGATGAT
1 GATGATGATGACGAT
*
671794 GAAGATGATGA
1 GATGATGATGA
671805 TCCAAAACAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
12 9 0.16
13 1 0.02
14 1 0.02
15 46 0.81
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (15 bp):
GATGATGATGACGAT
Found at i:671748 original size:27 final size:27
Alignment explanation
Indices: 671718--671801 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
671708 AAGATGAAGC
671718 TGACGATGAAGATGACGATGATGATGA
1 TGACGATGAAGATGACGATGATGATGA
* * *
671745 TGACGATGAAGCTGGCGATGAAGATGA
1 TGACGATGAAGATGACGATGATGATGA
* * *
671772 TGACGATGATGATGATGATGATGAAGA
1 TGACGATGAAGATGACGATGATGATGA
671799 TGA
1 TGA
671802 TGATCCAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.23
Consensus pattern (27 bp):
TGACGATGAAGATGACGATGATGATGA
Found at i:673799 original size:183 final size:184
Alignment explanation
Indices: 673147--674164 Score: 1819
Period size: 183 Copynumber: 5.7 Consensus size: 184
673137 CTTTCAACAT
*
673147 ATTATAAT-AAATAGATAATTTTGTAATA-AACCGGTAT-AATATACCGG--TTATGCGCGAA-A
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
673206 GGTCTACAACCTATATCGACACTTTTTAATATTATGTCGGTAC-TTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
673270 AATGTGTCGATACGATTTAAAAAAGTGTCGACA-TTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
673323 ATTATAATGTAATAGATAATTTTGTAATA-AACCGGTATAAATATACCGGTC-TATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
673386 GGTCTACAACCTATATCG--ACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
673449 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
673503 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
673568 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
673633 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
673687 ATTATAA-GTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
673751 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
673816 AATGTGTCGATACAATTTAAAAAAGTGTCGACA-TTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
673869 ATTATAATGTAATAGATAATTTTGT-A-ATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
673932 GG--TACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
673995 AATGTGTCGATACGATTT-AAAAAGTGTCGACATTTT--ACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
674046 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATA-CGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
674110 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
674165 CCATTTAAAA
Statistics
Matches: 818, Mismatches: 7, Indels: 30
0.96 0.01 0.04
Matches are distributed among these distances:
176 8 0.01
177 68 0.08
178 65 0.08
179 162 0.20
180 118 0.14
181 61 0.07
182 58 0.07
183 172 0.21
184 106 0.13
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:676738 original size:23 final size:23
Alignment explanation
Indices: 676707--676769 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
676697 ATAGGTAAAC
*
676707 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
676730 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
676753 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
676770 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:676777 original size:23 final size:23
Alignment explanation
Indices: 676707--676779 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
676697 ATAGGTAAAC
* * **
676707 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
676730 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
676753 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
676776 ATAT
1 ATAT
676780 GTAAAGTGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:676966 original size:29 final size:30
Alignment explanation
Indices: 676923--676989 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
676913 GTTACGGTAT
* *
676923 ATATTATTATTAAAT-TAAAA-ATTCTAAATA
1 ATATT-TTATAAAATATAAAACAATC-AAATA
676953 ATATTTTATAAAATATAAAACAATCAAATA
1 ATATTTTATAAAATATAAAACAATCAAATA
*
676983 ATTTTTT
1 ATATTTT
676990 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 21 0.66
31 3 0.09
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATTTTATAAAATATAAAACAATCAAATA
Found at i:677166 original size:23 final size:23
Alignment explanation
Indices: 677135--677197 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
677125 ATAGGTAAAC
*
677135 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
677158 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
677181 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
677198 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:677205 original size:23 final size:23
Alignment explanation
Indices: 677135--677207 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
677125 ATAGGTAAAC
* * **
677135 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
677158 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
677181 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
677204 ATAT
1 ATAT
677208 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:677235 original size:20 final size:20
Alignment explanation
Indices: 677210--677248 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
677200 GGTTATATTG
* *
677210 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
677230 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
677249 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:677620 original size:23 final size:23
Alignment explanation
Indices: 677557--677621 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
677547 ATAGGTAAAC
* *
677557 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
* **
677580 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
677603 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
677622 TATCTCGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:677845 original size:18 final size:18
Alignment explanation
Indices: 677824--677860 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
677814 GTAATTGGAG
677824 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
677842 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
677860 T
1 T
677861 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:677868 original size:24 final size:24
Alignment explanation
Indices: 677816--677862 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
677806 TTTCATATGT
* *
677816 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
677840 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
677863 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:689605 original size:20 final size:21
Alignment explanation
Indices: 689564--689607 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
689554 TAATTAAAAA
*
689564 TTATTTAAAATATTATTATTT
1 TTATTTAAAACATTATTATTT
689585 TTATTTAAAACATTA-TATTT
1 TTATTTAAAACATTATTATTT
689605 TTA
1 TTA
689608 ACATTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTAAAACATTATTATTT
Found at i:689892 original size:20 final size:20
Alignment explanation
Indices: 689867--689911 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
689857 GTCATTCAAT
* *
689867 TTTTTAAACCCCATACCGGA
1 TTTTTAAACCCCAGAACGGA
689887 TTTTTAAACCCCAGAACGGA
1 TTTTTAAACCCCAGAACGGA
689907 TTTTT
1 TTTTT
689912 TTCCGGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTTTAAACCCCAGAACGGA
Found at i:692408 original size:18 final size:18
Alignment explanation
Indices: 692385--692419 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
692375 GGATATTGAC
692385 GTGATAATTTATGATGAT
1 GTGATAATTTATGATGAT
692403 GTGATAATTTATGATGA
1 GTGATAATTTATGATGA
692420 CTAATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (18 bp):
GTGATAATTTATGATGAT
Found at i:697476 original size:39 final size:38
Alignment explanation
Indices: 697433--697527 Score: 154
Period size: 39 Copynumber: 2.4 Consensus size: 38
697423 TAACATTGAG
697433 ATGAAATAATTTAAGAAATAAAGAATTTAGAATGTTATT
1 ATGAAATAATTTAAGAAATAAAGAATTTAGAATGTTA-T
* *
697472 ATGAAATAATTTAATAAATTAAGAATTTAGAATGTTAT
1 ATGAAATAATTTAAGAAATAAAGAATTTAGAATGTTAT
697510 AGTGAAATAATTTAAGAA
1 A-TGAAATAATTTAAGAA
697528 TTAATAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
38 2 0.04
39 50 0.96
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.36
Consensus pattern (38 bp):
ATGAAATAATTTAAGAAATAAAGAATTTAGAATGTTAT
Found at i:697959 original size:31 final size:29
Alignment explanation
Indices: 697921--697979 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
697911 AAACTATATG
697921 TTTAGTACCTAAA-TTATCAAATTTATTTCAT
1 TTTAGTACCTAAACTT-TC--ATTTATTTCAT
*
697952 TTTAGTACTTAAACTTTCATTTATTTCA
1 TTTAGTACCTAAACTTTCATTTATTTCA
697980 AAATCATACG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 10 0.38
31 14 0.54
32 2 0.08
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTAGTACCTAAACTTTCATTTATTTCAT
Found at i:701025 original size:2 final size:2
Alignment explanation
Indices: 701020--701050 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
701010 TTTTTTATTA
701020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
701051 AATTAGTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:701361 original size:25 final size:25
Alignment explanation
Indices: 701309--701358 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
701299 TCGTCACTTC
*
701309 TAAAATTTTATAATTTATTATTTCT
1 TAAAATTTTATAAGTTATTATTTCT
701334 TAAAATTTTAT-AGTT-TTATCTTCT
1 TAAAATTTTATAAGTTATTAT-TTCT
701358 T
1 T
701359 TAACATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 8 0.35
25 11 0.48
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (25 bp):
TAAAATTTTATAAGTTATTATTTCT
Found at i:702759 original size:60 final size:60
Alignment explanation
Indices: 702664--702835 Score: 251
Period size: 60 Copynumber: 2.9 Consensus size: 60
702654 GTATTATATG
* * *
702664 TCCCTAAACTATAA-TCTTCATTTTAAATT-GATCTTTAAAGTTTTAAATATTTTAATTTCA
1 TCCCTAAACTATAACTC-TCATTTTAAATTAG-TCTTTAAACTTTTGAATATTCTAATTTCA
702724 TCCCTAAACTATAACTCTCATTTTAAATTAGTCTTTAAACTTTTGAATATTCTAATTTCA
1 TCCCTAAACTATAACTCTCATTTTAAATTAGTCTTTAAACTTTTGAATATTCTAATTTCA
* *
702784 TCCCTAAACTATGACCCTC-TTTCTAAATTAGTCTTTAAACTTTTGAATATTC
1 TCCCTAAACTATAACTCTCATTT-TAAATTAGTCTTTAAACTTTTGAATATTC
702836 CGATTTCACT
Statistics
Matches: 104, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
59 3 0.03
60 98 0.94
61 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (60 bp):
TCCCTAAACTATAACTCTCATTTTAAATTAGTCTTTAAACTTTTGAATATTCTAATTTCA
Found at i:703007 original size:29 final size:29
Alignment explanation
Indices: 702965--703023 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
702955 GTGTGGCCGT
702965 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
702994 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
703023 A
1 A
703024 TTCATGCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.34, G:0.36, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:703275 original size:29 final size:29
Alignment explanation
Indices: 703240--703326 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
703230 GTTGGCTGGT
*
703240 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
703269 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
703298 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
703327 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Done.