Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002694.1 Hibiscus syriacus cultivar Beakdansim tig00005566_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: 187373
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2649 original size:144 final size:140
Alignment explanation
Indices: 2384--2673 Score: 392
Period size: 141 Copynumber: 2.0 Consensus size: 140
2374 GAGTCGAGGG
* * * *
2384 TCTACGCGGTCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGTCTTTGAGGCACATACT
1 TCTACGCGGTCTTCGGGA-ATA-GTATATTCTGTGGAACATGTATGAGTCTTTAAGACACATACT
* *
2449 TGGTCCTTAGTATATGTATATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATATGGC
64 TGATCCCTAGTATATGTATATTCTTAAGGAATGATA-GTGGTCCTTATGGACATTATTATATGGC
2514 ACTACGGTGCAAT
128 ACTACGGTGCAAT
*
2527 TCTACGCGGTCCTTCGGG-ATA-TATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
1 TCTACGCGGT-CTTCGGGAATAGTATATTCTGTGGAACATGTATG-AGTCTT-TAAGACACATAC
2590 TTGATCCCTAGTATATGTATATAAT-TCTAAGGAATGATA-T-GTCCTTATGGACATTATTATAT
63 TTGATCCCTAGTATATGTATAT--TCT-TAAGGAATGATAGTGGTCCTTATGGACATTATTATAT
*
2652 GGCACTACGGTGTAAT
125 GGCACTACGGTGCAAT
2668 TCTACG
1 TCTACG
2674 TGCACTTCGG
Statistics
Matches: 133, Mismatches: 8, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
140 19 0.14
141 49 0.37
142 34 0.26
143 11 0.08
144 20 0.15
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (140 bp):
TCTACGCGGTCTTCGGGAATAGTATATTCTGTGGAACATGTATGAGTCTTTAAGACACATACTTG
ATCCCTAGTATATGTATATTCTTAAGGAATGATAGTGGTCCTTATGGACATTATTATATGGCACT
ACGGTGCAAT
Found at i:3493 original size:2 final size:2
Alignment explanation
Indices: 3488--3529 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
3478 TGGGTGGAAG
3488 TA TA TA TA TA -A TA TA -A TA TA TA TA TA TA -A 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
3527 TA T
1 TA T
3530 TTAATAACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3516 original size:13 final size:13
Alignment explanation
Indices: 3489--3528 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
3479 GGGTGGAAGT
3489 ATATATATAATATA
1 ATATATAT-ATATA
3503 ATATATATATATA
1 ATATATATATATA
3516 ATATATATATATA
1 ATATATATATATA
3529 TTTAATAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATATATATATA
Found at i:7335 original size:64 final size:63
Alignment explanation
Indices: 7267--7387 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 63
7257 TTGTTTCAAG
* * * *
7267 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA
* *
7331 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATG
7388 GAATTATGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 17 0.33
64 34 0.67
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCCATCA
Found at i:9130 original size:17 final size:17
Alignment explanation
Indices: 9104--9136 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9094 CCTTGATTGA
9104 TGAATCTAAATTAAGAG
1 TGAATCTAAATTAAGAG
*
9121 TGAATTTAAATTAAGA
1 TGAATCTAAATTAAGA
9137 TATTCTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.33
Consensus pattern (17 bp):
TGAATCTAAATTAAGAG
Found at i:10634 original size:65 final size:65
Alignment explanation
Indices: 10498--10658 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 65
10488 GTGCACTAAG
* *
10498 TGTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGTCT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGTCA
* * *
10562 TGAGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATC-AGTGCATGG
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGA-TGCAT-G
10625 T-A
63 TCA
* *
10627 TGTGCATCGCTGCATAAAATGCATTCAATGTT
1 TGTGCATCGATGCATAAAATGCATTCGATGTT
10659 CAATTTATTC
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 28 0.34
65 50 0.60
66 5 0.06
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (65 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGTCA
Found at i:23149 original size:64 final size:65
Alignment explanation
Indices: 23081--23205 Score: 182
Period size: 64 Copynumber: 1.9 Consensus size: 65
23071 ATGCACTAAG
* * * *
23081 TGTGCATCGATGCATTAAATGCATTCGATG-TTTCA-AAATAGCCTTAGTGCATCGATGCATGTC
1 TGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTACATCGATGCATGTC
23144 T
65 T
*
23145 TGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAACCCTGAGTACATCGATGCAT
1 TGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGAGTACATCGATGCAT
23206 AAAATGCATT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
64 28 0.52
65 23 0.43
66 3 0.06
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (65 bp):
TGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGAGTACATCGATGCATGTCT
Found at i:34537 original size:33 final size:33
Alignment explanation
Indices: 34495--34560 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
34485 CATCAGCAAA
34495 TCCGAGTTAAGATCGATCCAGGCTGGGAACACT
1 TCCGAGTTAAGATCGATCCAGGCTGGGAACACT
34528 TCCGAGTTAAGATCGATCCAGGCTGGGAACACT
1 TCCGAGTTAAGATCGATCCAGGCTGGGAACACT
34561 GATCCTCCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (33 bp):
TCCGAGTTAAGATCGATCCAGGCTGGGAACACT
Found at i:37019 original size:15 final size:15
Alignment explanation
Indices: 36999--37028 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
36989 TATCACAATC
36999 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
37014 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
37029 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:45405 original size:26 final size:26
Alignment explanation
Indices: 45369--45441 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
45359 TGGCCGATGC
*
45369 TTGTAAATGAAAACTAAAACAAATTA
1 TTGTAAATGAAAACAAAAACAAATTA
45395 TTGTAAATGAAAACAAAAACAAATTA
1 TTGTAAATGAAAACAAAAACAAATTA
* *
45421 TTGCAAATGAAAACAGAAACA
1 TTGTAAATGAAAACAAAAACA
45442 TGCAATTGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (26 bp):
TTGTAAATGAAAACAAAAACAAATTA
Found at i:49714 original size:39 final size:39
Alignment explanation
Indices: 49671--49746 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
49661 TAAGAGGTTA
49671 AGAAAGAAGTAA-AAAAGGTATAAAACTATTGAAATTTAG
1 AGAAAGAAGTAACAAAA-GTATAAAACTATTGAAATTTAG
* *
49710 AGAAAGAAGTAACAACAGTATTAAACTATTGAAATTT
1 AGAAAGAAGTAACAAAAGTATAAAACTATTGAAATTT
49747 GGGAATAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 31 0.91
40 3 0.09
ACGTcount: A:0.54, C:0.05, G:0.16, T:0.25
Consensus pattern (39 bp):
AGAAAGAAGTAACAAAAGTATAAAACTATTGAAATTTAG
Found at i:51281 original size:60 final size:58
Alignment explanation
Indices: 51214--51391 Score: 150
Period size: 57 Copynumber: 3.0 Consensus size: 58
51204 CATATGTGCT
51214 TAAACTATAACTTTTATTTTAAATTGGTCCTTAAATTTTTGAATATTCTAATTTCATCCC
1 TAAACTATAACTTTTATTTTAAATTGGT-C-TAAATTTTTGAATATTCTAATTTCATCCC
* ** * * * *
51274 TAAACTATTAA-TCTTAAATTAAATTAGTC-AAACTATTGAACATT-TCAATTTCAT-CC
1 TAAACTA-TAACTTTTATTTTAAATTGGTCTAAATTTTTGAATATTCT-AATTTCATCCC
* * *
51330 TCAAACTATAACCTTTATTCTAAATTGGTCTCCAAACTTTTT-AATCATTCCAATTTCATCCC
1 T-AAACTATAACTTTTATTTTAAATTGGTCT--AAA-TTTTTGAAT-ATTCTAATTTCATCCC
51392 AATTTCATCC
Statistics
Matches: 90, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
56 7 0.08
57 38 0.42
59 1 0.01
60 25 0.28
61 17 0.19
62 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (58 bp):
TAAACTATAACTTTTATTTTAAATTGGTCTAAATTTTTGAATATTCTAATTTCATCCC
Found at i:51623 original size:60 final size:59
Alignment explanation
Indices: 51516--51627 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 59
51506 AGTACATATG
* * * * * *
51516 TATAGTTTAGGATGAAATTGGATTTTTAAAAAGTTTGAAGATCAATTTAGAATGAAGGT
1 TATAGTTTAGGATAAAATTGAAATGTTAAAAACTTTAAAGATCAATTTAGAATGAAGGT
*
51575 TATAGTTTAGGGATAAAATTGAAATGTTCAAAACTTTAAAGAAT-AATTTAGAA
1 TATAGTTTA-GGATAAAATTGAAATGTTAAAAACTTTAAAG-ATCAATTTAGAA
51628 CCATAGTCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
59 9 0.20
60 33 0.75
61 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.36
Consensus pattern (59 bp):
TATAGTTTAGGATAAAATTGAAATGTTAAAAACTTTAAAGATCAATTTAGAATGAAGGT
Found at i:51805 original size:18 final size:18
Alignment explanation
Indices: 51782--51835 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
51772 AATATTTTTA
51782 TATTTTCTATTAATAATT
1 TATTTTCTATTAATAATT
51800 TA-TTT-TATCTAAT-ATT
1 TATTTTCTAT-TAATAATT
51816 TATATTTCTATTAATAATT
1 TAT-TTTCTATTAATAATT
51835 T
1 T
51836 GTTGTCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
16 8 0.26
17 7 0.23
18 9 0.29
19 7 0.23
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTTCTATTAATAATT
Found at i:64037 original size:20 final size:20
Alignment explanation
Indices: 64008--64050 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
63998 ATATGAGAAT
*
64008 AAATATAATTGTA-AAAATAA
1 AAATAAAATT-TACAAAATAA
*
64028 AAATAAAATTTACAACATAA
1 AAATAAAATTTACAAAATAA
64048 AAA
1 AAA
64051 ACTATTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (20 bp):
AAATAAAATTTACAAAATAA
Found at i:64280 original size:30 final size:29
Alignment explanation
Indices: 64212--64332 Score: 143
Period size: 30 Copynumber: 4.1 Consensus size: 29
64202 CTGGAAGTGC
* * *
64212 CTAAATAGCAAAAATAGAAATTTAAAGGA
1 CTAAATAGCAAAAACAAAAAGTTAAAGGA
64241 CTAAATAGCAAAAACAAAAAGTTAAAGGA
1 CTAAATAGCAAAAACAAAAAGTTAAAGGA
* * * *
64270 CTAGAATAGCAAAAATAGAAACTTAAAAGA
1 CTA-AATAGCAAAAACAAAAAGTTAAAGGA
* *
64300 CTAAAATAGCTAAAACAAAAAGTTAATGGA
1 CT-AAATAGCAAAAACAAAAAGTTAAAGGA
64330 CTA
1 CTA
64333 CACAGTAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 30 0.39
30 46 0.60
31 1 0.01
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (29 bp):
CTAAATAGCAAAAACAAAAAGTTAAAGGA
Found at i:64286 original size:59 final size:60
Alignment explanation
Indices: 64215--64332 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
64205 GAAGTGCCTA
* *
64215 AATAGCAAAAATAGAAATTTAAAGGACT-AAATAGCAAAAACAAAAAGTTAAAGGACTAG
1 AATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCAAAAACAAAAAGTTAAAGGACTAG
* *
64274 AATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTAAAACAAAAAGTTAATGGACTA
1 AATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCAAAAACAAAAAGTTAAAGGACTA
64333 CACAGTAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
59 26 0.48
60 28 0.52
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (60 bp):
AATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCAAAAACAAAAAGTTAAAGGACTAG
Found at i:65861 original size:3 final size:3
Alignment explanation
Indices: 65853--65916 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
65843 ATTGTAATGT
* * * *
65853 TAA TAA TAA CAA TAA TAA CAA CAAA TAA TAA TAA TCA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
65898 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
65917 TTTTTGTAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.92
4 2 0.04
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:66739 original size:137 final size:134
Alignment explanation
Indices: 66108--66739 Score: 631
Period size: 137 Copynumber: 4.7 Consensus size: 134
66098 GGTCTGGTCG
* * * * ** * *
66108 TCTAAGGGTGACACAGCTCCTACGAGATGAGGAGATTTGGTCGGTGGATGACACGACTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACGC
* * * ** * *
66173 GATGAAGA-GTTC-TGGCCATCTTTAGCA-GGGGTGATAACACGATTCCTACGCGATGAGGACAA
66 GATGAGGACG-GCAT-GCCATCTTTAGGATAAGGTGATAACACGGTTCCTACGTGATGAGGAC-A
*
66235 CTAGTTA
128 CTGGTTA
* * * * * *
66242 TC--AGGGATGACACAGCTCCTACGTGATGAGGAGGTCTGGTCAGTGGATGACACAGTTCCTATG
1 TCTAAGGG-TGACACGGCTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACG
* * * * * * ** *
66305 TGATGAGGATGGCATACCATCTTTA-G--CA--TGATAACATGGTTCATATATGATGAGGATGAC
65 CGATGAGGACGGCATGCCATCTTTAGGATAAGGTGATAACACGGTTCCTACGTGATGAGGA-CAC
66365 TGGTTA
129 TGGTTA
*
66371 TC--AGGGATGACACGACTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACG
1 TCTAAGGG-TGACACGGCTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACG
* * ** *
66434 CGATGTGGACGGCAAGCCATCTTTATTTATGAGGTAGATAACACGGTTCCTACGTGATGAGGACG
65 CGATGAGGACGGCATGCCATCTTTA-GGATAAGGT-GATAACACGGTTCCTACGTGATGAGGAC-
66499 ACTGGTTA
127 ACTGGTTA
* * * *
66507 TCTAAGGGTAACACGACTCCTACGTGATAAGGAGGTTTGGTCAGGGGATGACACGGTTCCTACGC
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACGC
* * *
66572 GATGAGAACGGCATGCCATCTTTATTGATAAGGTAGATAACACGGTTCTTACGTGATGAGGACAT
66 GATGAGGACGGCATGCCATCTTTA-GGATAAGGT-GATAACACGGTTCCTACGTGATGAGGACA-
66637 CTGGTTA
128 CTGGTTA
* * *
66644 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGTTCCTATGC
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACGC
*
66709 GATGAGGACGACATGCCATCTTTAGGGATAA
66 GATGAGGACGGCATGCCATCTTTA-GGATAA
66740 TGGTTTCAAG
Statistics
Matches: 421, Mismatches: 62, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
129 105 0.25
132 4 0.01
133 66 0.16
134 4 0.01
135 1 0.00
136 34 0.08
137 203 0.48
138 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (134 bp):
TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACGC
GATGAGGACGGCATGCCATCTTTAGGATAAGGTGATAACACGGTTCCTACGTGATGAGGACACTG
GTTA
Found at i:66779 original size:29 final size:30
Alignment explanation
Indices: 66735--66791 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
66725 CATCTTTAGG
*
66735 GATAATGGTTTCAAGAGAAACTGACTCATA
1 GATAATGGCTTCAAGAGAAACTGACTCATA
* *
66765 GATAAT-GCTTCAAGAGAAGCTGTCTCA
1 GATAATGGCTTCAAGAGAAACTGACTCA
66792 AAAGAGACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (30 bp):
GATAATGGCTTCAAGAGAAACTGACTCATA
Found at i:66948 original size:65 final size:67
Alignment explanation
Indices: 66836--66972 Score: 191
Period size: 67 Copynumber: 2.1 Consensus size: 67
66826 ATATGTTTGT
*
66836 TTTGTTTCAAGGGAAACATAATCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAA
1 TTTGTTTCAAGAGAAACATAATCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAA
66901 AC
66 AC
*
66903 TTTGTTTCCAGAGAAACA-AACTCAAAGA-TTTTTT-TCAAAAGAAATTGTCTC--GAGAG--AA
1 TTTGTTTCAAGAGAAACATAA-TCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAA
66961 AA-
65 AAC
66963 TTTGTTTCAA
1 TTTGTTTCAA
66973 AATAAATAAC
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
60 9 0.14
61 4 0.06
63 5 0.08
65 17 0.26
66 8 0.12
67 23 0.35
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (67 bp):
TTTGTTTCAAGAGAAACATAATCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAA
AC
Found at i:67787 original size:27 final size:27
Alignment explanation
Indices: 67746--67809 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
67736 GCTGCTCAAT
67746 CAGAAGGTAATCTGGTCATGAAAGAAC
1 CAGAAGGTAATCTGGTCATGAAAGAAC
* *
67773 CATAAGGTAATCTGGTTATGAAAGAAC
1 CAGAAGGTAATCTGGTCATGAAAGAAC
*
67800 TAGAAGGTAA
1 CAGAAGGTAA
67810 ACCTCATGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (27 bp):
CAGAAGGTAATCTGGTCATGAAAGAAC
Found at i:72078 original size:18 final size:19
Alignment explanation
Indices: 72053--72099 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
72043 GCTTCTTATC
*
72053 TTTTTTTCTTT-CT-TTTG
1 TTTTTTTCTTTGATATTTG
72070 TTCTTTTTCTTTGATATTTG
1 TT-TTTTTCTTTGATATTTG
72090 TTTTTTTCTT
1 TTTTTTTCTT
72100 CTTCTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 2 0.08
18 9 0.35
19 9 0.35
20 6 0.23
ACGTcount: A:0.04, C:0.11, G:0.06, T:0.79
Consensus pattern (19 bp):
TTTTTTTCTTTGATATTTG
Found at i:72114 original size:25 final size:24
Alignment explanation
Indices: 72051--72119 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
72041 GTGCTTCTTA
*
72051 TCTT-TTTTTCTTTCTTTTGTTCT
1 TCTTCTTTTTCTTTGTTTTGTTCT
* * * *
72074 TTTTCTTTGATATTTGTTTTTTTCT
1 TCTTCTTT-TTCTTTGTTTTGTTCT
72099 TCTTCTTTTCTCTTTGTTTTG
1 TCTTCTTTT-TCTTTGTTTTG
72120 ATTTGATCTT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
23 3 0.09
24 3 0.09
25 28 0.82
ACGTcount: A:0.03, C:0.14, G:0.07, T:0.75
Consensus pattern (24 bp):
TCTTCTTTTTCTTTGTTTTGTTCT
Found at i:73717 original size:43 final size:41
Alignment explanation
Indices: 73659--73801 Score: 159
Period size: 42 Copynumber: 3.4 Consensus size: 41
73649 TCGTTTTTTA
**
73659 ACAAACGCCACAATAGAGTGGTAAATTAGTGGTCGTTTATACC
1 ACAAACGCCGTAATAGA-TGGTAAATTAGTGG-CGTTTATACC
73702 ACAAACGCCGTAATAGAT--TAATATATAGTGGCGTTT-TAGCC
1 ACAAACGCCGTAATAGATGGTAA-AT-TAGTGGCGTTTATA-CC
* * *
73743 A-AAACGCCGTAGTAGATCGGTAAATTAGCGGCGTTTATAAC
1 ACAAACGCCGTAATAGAT-GGTAAATTAGTGGCGTTTATACC
73784 ACAAACGCCGTAATAGAT
1 ACAAACGCCGTAATAGAT
73802 TACACATATA
Statistics
Matches: 86, Mismatches: 6, Indels: 17
0.79 0.06 0.16
Matches are distributed among these distances:
40 20 0.23
41 22 0.26
42 26 0.30
43 18 0.21
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (41 bp):
ACAAACGCCGTAATAGATGGTAAATTAGTGGCGTTTATACC
Found at i:73748 original size:83 final size:83
Alignment explanation
Indices: 73661--73816 Score: 226
Period size: 83 Copynumber: 1.9 Consensus size: 83
73651 GTTTTTTAAC
* * *
73661 AAACGCCACAATAGAGT-GGTAAATTAGTGGTCGTTTATACCACAAACGCCGTAATAGATTA-AT
1 AAACGCCACAATAGA-TCGGTAAATTAGCGG-CGTTTATAACACAAACGCCGTAATAGATTACAC
73724 ATATAGTGGCGTTTTAGCCA
64 ATATAGTGGCGTTTTAGCCA
** *
73744 AAACGCCGTAGTAGATCGGTAAATTAGCGGCGTTTATAACACAAACGCCGTAATAGATTACACAT
1 AAACGCCACAATAGATCGGTAAATTAGCGGCGTTTATAACACAAACGCCGTAATAGATTACACAT
73809 ATAGTGGC
66 ATAGTGGC
73817 ATTTATTCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
82 30 0.46
83 35 0.54
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (83 bp):
AAACGCCACAATAGATCGGTAAATTAGCGGCGTTTATAACACAAACGCCGTAATAGATTACACAT
ATAGTGGCGTTTTAGCCA
Found at i:73753 original size:40 final size:40
Alignment explanation
Indices: 73680--73822 Score: 150
Period size: 42 Copynumber: 3.5 Consensus size: 40
73670 AATAGAGTGG
73680 TAAAT-TAGTGGTCGTTTATACCACAAACGCCGTAATAGAT
1 TAAATATAGTGG-CGTTTATACCACAAACGCCGTAATAGAT
*
73720 TAATATATAGTGGCGTTT-TAGCCA-AAACGCCGTAGTAGAT
1 TAA-ATATAGTGGCGTTTATA-CCACAAACGCCGTAATAGAT
* *
73760 CGGTAAAT-TAGCGGCGTTTATAACACAAACGCCGTAATAGAT
1 ---TAAATATAGTGGCGTTTATACCACAAACGCCGTAATAGAT
*
73802 TACACATATAGTGGCATTTAT
1 TA-A-ATATAGTGGCGTTTAT
73823 TCTTAAAAAG
Statistics
Matches: 86, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
39 2 0.02
40 21 0.24
41 24 0.28
42 36 0.42
43 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (40 bp):
TAAATATAGTGGCGTTTATACCACAAACGCCGTAATAGAT
Found at i:73895 original size:41 final size:40
Alignment explanation
Indices: 73836--73986 Score: 198
Period size: 41 Copynumber: 3.7 Consensus size: 40
73826 TAAAAAGCCT
* *
73836 CAATAGT-TATAATAAATAGTGGCATTTTTAGACAAACGCCG
1 CAATAGTGT-TAATCAATAGTGGCGTTTTTA-ACAAACGCCG
* *
73877 CAATAATGTTAATCAATAGTGGCGTTTTTATAAAAACGCCG
1 CAATAGTGTTAATCAATAGTGGCGTTTTTA-ACAAACGCCG
* *
73918 CAATAGTTTTAATCAATAGTGGCGTTTTTTAACAAACGCCA
1 CAATAGTGTTAATCAATAGTGGCG-TTTTTAACAAACGCCG
73959 CAATAGTG-TAATCAATAGTGGCGTTTTT
1 CAATAGTGTTAATCAATAGTGGCGTTTTT
73987 TTGTATAAAC
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
39 5 0.05
40 15 0.15
41 71 0.72
42 7 0.07
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (40 bp):
CAATAGTGTTAATCAATAGTGGCGTTTTTAACAAACGCCG
Found at i:73987 original size:41 final size:41
Alignment explanation
Indices: 73809--73988 Score: 188
Period size: 41 Copynumber: 4.4 Consensus size: 41
73799 GATTACACAT
* * * *
73809 ATAGTGGCATTTATTCTTAAAAA-GCCTCAATAGTTATAATAA
1 ATAGTGGCGTTT-TT-TTAAAAACGCCGCAATAGTTGTAATCA
* ** * *
73851 ATAGTGGCATTTTTAGACAAACGCCGCAATA-ATGTTAATCA
1 ATAGTGGCGTTTTTTTAAAAACGCCGCAATAGTTG-TAATCA
* *
73892 ATAGTGGCGTTTTTATAAAAACGCCGCAATAGTTTTAATCA
1 ATAGTGGCGTTTTTTTAAAAACGCCGCAATAGTTGTAATCA
*
73933 ATAGTGGCG-TTTTTTAACAAACGCCACAATAG-TGTAATCA
1 ATAGTGGCGTTTTTTTAA-AAACGCCGCAATAGTTGTAATCA
73973 ATAGTGGCGTTTTTTT
1 ATAGTGGCGTTTTTTT
73989 GTATAAACAC
Statistics
Matches: 118, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
40 28 0.24
41 77 0.65
42 13 0.11
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (41 bp):
ATAGTGGCGTTTTTTTAAAAACGCCGCAATAGTTGTAATCA
Found at i:73987 original size:82 final size:81
Alignment explanation
Indices: 73809--73988 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
73799 GATTACACAT
* *
73809 ATAGTGGCATTTATTCTTAAAAAGCCTCAATAGTTATAATAAATAGTGGCATTTTTAGACAAACG
1 ATAGTGGCGTTT-TT-TTAAAAAGCCGCAATAGTTATAATAAATAGTGGCATTTTTAGACAAACG
*
73874 CCGCAATAATGTTAATCA
64 CCACAATAATGTTAATCA
* * * *
73892 ATAGTGGCGTTTTTATAAAAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTTA-ACAAACG
1 ATAGTGGCGTTTTTTTAAAAA-GCCGCAATAGTTATAATAAATAGTGGC-ATTTTTAGACAAACG
*
73956 CCACAATAGTG-TAATCA
64 CCACAATAATGTTAATCA
73973 ATAGTGGCGTTTTTTT
1 ATAGTGGCGTTTTTTT
73989 GTATAAACAC
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
81 27 0.31
82 42 0.49
83 17 0.20
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (81 bp):
ATAGTGGCGTTTTTTTAAAAAGCCGCAATAGTTATAATAAATAGTGGCATTTTTAGACAAACGCC
ACAATAATGTTAATCA
Found at i:75179 original size:41 final size:42
Alignment explanation
Indices: 75094--75197 Score: 129
Period size: 41 Copynumber: 2.5 Consensus size: 42
75084 GCCGCTATAA
* *
75094 ACTCATACTTTAGTGGCGTTTTGAATGCAAATGCCACTAAAG
1 ACTCGTACTTTAGTGGCGTTTTGAATACAAATGCCACTAAAG
* * * ** *
75136 ACTTGTACTTTAGTGGCGTTTT-TATACAAATGTCGTTATAG
1 ACTCGTACTTTAGTGGCGTTTTGAATACAAATGCCACTAAAG
75177 ACTCGTACTTTAGTGGCGTTT
1 ACTCGTACTTTAGTGGCGTTT
75198 GTATTTACAA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 33 0.62
42 20 0.38
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (42 bp):
ACTCGTACTTTAGTGGCGTTTTGAATACAAATGCCACTAAAG
Found at i:81518 original size:21 final size:21
Alignment explanation
Indices: 81469--81519 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
81459 AAGTAGAGAA
*
81469 AGAAGCAACGACAGCACAGAG
1 AGAAGCAGCGACAGCACAGAG
*
81490 AGAAGCAGCGGCAGCACAGAG
1 AGAAGCAGCGACAGCACAGAG
81511 AGAAGCAGC
1 AGAAGCAGC
81520 ATATCAGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.24, G:0.33, T:0.00
Consensus pattern (21 bp):
AGAAGCAGCGACAGCACAGAG
Found at i:82042 original size:43 final size:43
Alignment explanation
Indices: 81932--82300 Score: 147
Period size: 43 Copynumber: 8.6 Consensus size: 43
81922 TTTTTAGTAG
* * **
81932 AAACGCCGCAAAACATCAATACCTACTGTGGCGTTTGTGAAAA
1 AAACGCCGCTAAACATCAACACCTACTACGGCGTTTGTGAAAA
**
81975 AAACGCCG-TAAGACATCAACACCTACTACGGCGTTT-TAGCGAA
1 AAACGCCGCTAA-ACATCAACACCTACTACGGCGTTTGT-GAAAA
* * * ***
82018 AAACGCCGCTAAACATCATA-ACCTATTGCGACGTTTGTCTGAA
1 AAACGCCGCTAAACATCA-ACACCTACTACGGCGTTTGTGAAAA
* * * * * * * * *
82061 AAACGCTGCTAAATATTAACACCTATTGCGGCATTT-TTATGAC
1 AAACGCCGCTAAACATCAACACCTACTACGGCGTTTGTGA-AAA
* * * ***
82104 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGAA
1 AAACGCCGCTAAACATCAACACCTACTACGGCGTTTGTGAAAA
* * * * * * * * *
82147 AAACACTGCTAAATATCAACACCTATTGCGGCATTT-TTATGAC
1 AAACGCCGCTAAACATCAACACCTACTACGGCGTTTGTGA-AAA
* * * ** * * *
82190 AAACGCCGCTAAATATCAATACCTATTGTGGCGTTT-TTATGAC
1 AAACGCCGCTAAACATCAACACCTACTACGGCGTTTGTGA-AAA
* * * * * * * *
82233 AAACGCCGCTAAATAGCAACACCTATTACGCCGTTTATCACAC
1 AAACGCCGCTAAACATCAACACCTACTACGGCGTTTGTGAAAA
* * *
82276 AAACGCCTCTAAATATCAATACCTA
1 AAACGCCGCTAAACATCAACACCTA
82301 TTGCGGAATT
Statistics
Matches: 270, Mismatches: 46, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
42 6 0.02
43 256 0.95
44 8 0.03
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAACATCAACACCTACTACGGCGTTTGTGAAAA
Found at i:82042 original size:86 final size:85
Alignment explanation
Indices: 81917--82306 Score: 344
Period size: 86 Copynumber: 4.5 Consensus size: 85
81907 AGACTTGTAC
* * * *
81917 CGGCATTTTTA-GTAGAAACGCCGCAAAACATCAATACCTACTGTGGCGTTTGTGAAAAAAACGC
1 CGGCATTTTTATG-ACAAACGCCGCTAAACATCAATACCTATTGCGGCGTTTGTGAAAAAAACGC
* * *
81981 CGTAAGACATCAACACCTACTA
65 CGTAA-ATATCAACACCTATTG
* * * * ***
82003 CGGC-GTTTTAGCGAAAAACGCCGCTAAACATC-ATAACCTATTGCGACGTTTGTCTGAAAAACG
1 CGGCATTTTTA-TGACAAACGCCGCTAAACATCAAT-ACCTATTGCGGCGTTTGTGAAAAAAACG
* *
82066 CTGCTAAATATTAACACCTATTG
64 CCG-TAAATATCAACACCTATTG
* * *
82089 CGGCATTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGAAAAACACT
1 CGGCATTTTTATGACAAACGCCGCTAAACATCAATACCTATTGCGGCGTTTG--TGAAAAAAAC-
82154 G-C-TAAATATCAACACCTATTG
63 GCCGTAAATATCAACACCTATTG
* * * * *
82175 CGGCATTTTTATGACAAACGCCGCTAAATATCAATACCTATTGTGGCGTTT-TTATGACAAACGC
1 CGGCATTTTTATGACAAACGCCGCTAAACATCAATACCTATTGCGGCGTTTGTGA-AAAAAACGC
* *
82239 CGCTAAATAGCAACACCTATTA
65 CG-TAAATATCAACACCTATTG
* * * * * *
82261 CGCCGTTTATCA-CACAAACGCCTCTAAATATCAATACCTATTGCGG
1 CGGCATTT-TTATGACAAACGCCGCTAAACATCAATACCTATTGCGG
82307 AATTTTTTTT
Statistics
Matches: 250, Mismatches: 40, Indels: 28
0.79 0.13 0.09
Matches are distributed among these distances:
83 3 0.01
84 5 0.02
85 7 0.03
86 216 0.86
87 12 0.05
88 6 0.02
89 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (85 bp):
CGGCATTTTTATGACAAACGCCGCTAAACATCAATACCTATTGCGGCGTTTGTGAAAAAAACGCC
GTAAATATCAACACCTATTG
Found at i:82301 original size:43 final size:43
Alignment explanation
Indices: 81975--82306 Score: 334
Period size: 43 Copynumber: 7.7 Consensus size: 43
81965 TTTGTGAAAA
* * * * *
81975 AAACGCCG-TAAGACATCAACACCTACTACGGCGTTTT-AGCGAA
1 AAACGCCGCTAA-ATATCAACACCTATTGCGGCGTTTTCA-TGAC
* * *
82018 AAACGCCGCTAAACATCATA-ACCTATTGCGACGTTTGTC-TGAA
1 AAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTT-TCATGAC
* * * *
82061 AAACGCTGCTAAATATTAACACCTATTGCGGCATTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTCATGAC
*
82104 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTC-TGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT-TCATGAC
* * * *
82147 AAACACTGCTAAATATCAACACCTATTGCGGCATTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTCATGAC
* * *
82190 AAACGCCGCTAAATATCAATACCTATTGTGGCGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTCATGAC
* * * *
82233 AAACGCCGCTAAATAGCAACACCTATTACGCCGTTTATCA-CAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT-TCATGAC
* *
82276 AAACGCCTCTAAATATCAATACCTATTGCGG
1 AAACGCCGCTAAATATCAACACCTATTGCGG
82307 AATTTTTTTT
Statistics
Matches: 242, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
42 3 0.01
43 231 0.95
44 8 0.03
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTCATGAC
Found at i:82306 original size:129 final size:128
Alignment explanation
Indices: 81917--82313 Score: 401
Period size: 129 Copynumber: 3.1 Consensus size: 128
81907 AGACTTGTAC
* * * * * * *
81917 CGGCATTTTTA-GTAGAAACGCCGCAAAACATCAATACCTACTGTGGCGTTTGTGA-AAAAAACG
1 CGGCATTTTTATG-AAAAACGCCGCTAAATATCAATACCTATTGTGGCGTTT-TTATGACAAACG
* * * *
81980 CCG-TAAGACATCAACACCTACTACGGCGTTTT-AGCGAAAAACGCCGCTAAACATC-ATAACCT
64 CCGCTAA-ATATCAACACCTATTACGGCGTTTTCA-C-AAAAACGCCTCTAAATATCAAT-ACCT
82042 ATTG
125 ATTG
* * * * * * * * *
82046 CGACGTTTGTCTGAAAAACGCTGCTAAATATTAACACCTATTGCGGCATTTTTATGACAAACGCC
1 CGGCATTTTTATGAAAAACGCCGCTAAATATCAATACCTATTGTGGCGTTTTTATGACAAACGCC
* ** * *
82111 GCTAAATATCAACACCTATTGCGGCGTTTGTCTGAAAAAC-ACTGCTAAATATCAACACCTATTG
66 GCTAAATATCAACACCTATTACGGCGTTT-TCACAAAAACGCCT-CTAAATATCAATACCTATTG
*
82175 CGGCATTTTTATGACAAACGCCGCTAAATATCAATACCTATTGTGGCGTTTTTATGACAAACGCC
1 CGGCATTTTTATGAAAAACGCCGCTAAATATCAATACCTATTGTGGCGTTTTTATGACAAACGCC
* * *
82240 GCTAAATAGCAACACCTATTACGCCGTTTATCACACAAACGCCTCTAAATATCAATACCTATTG
66 GCTAAATATCAACACCTATTACGGCGTTT-TCACAAAAACGCCTCTAAATATCAATACCTATTG
*
82304 CGGAATTTTT
1 CGGCATTTTT
82314 TTTGTGAAAA
Statistics
Matches: 215, Mismatches: 45, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
128 3 0.01
129 204 0.95
130 8 0.04
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (128 bp):
CGGCATTTTTATGAAAAACGCCGCTAAATATCAATACCTATTGTGGCGTTTTTATGACAAACGCC
GCTAAATATCAACACCTATTACGGCGTTTTCACAAAAACGCCTCTAAATATCAATACCTATTG
Found at i:84796 original size:20 final size:20
Alignment explanation
Indices: 84771--84874 Score: 100
Period size: 20 Copynumber: 5.0 Consensus size: 20
84761 CAGAACCCGT
84771 GGGGGTATCGATTCCCTCTA
1 GGGGGTATCGATTCCCTCTA
84791 GGGGGTATCGATTCCCTCTA
1 GGGGGTATCGATTCCCTCTA
* * *
84811 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGTATCGATT-CCC-TC-TA
* * * *
84834 AGGGGAATCGGTTCCTCTTTAA
1 GGGGGTATCGATTCC-CTCT-A
84856 GGGGGTATCGATTCCCTCT
1 GGGGGTATCGATTCCCTCT
84875 GCACCAAAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
20 31 0.45
21 6 0.09
22 18 0.26
23 14 0.20
ACGTcount: A:0.17, C:0.24, G:0.30, T:0.29
Consensus pattern (20 bp):
GGGGGTATCGATTCCCTCTA
Found at i:88585 original size:23 final size:23
Alignment explanation
Indices: 88530--88573 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
88520 ATCTTATATG
*
88530 GCACTACGGTGCAATTCTACGCA
1 GCACTTCGGTGCAATTCTACGCA
88553 GCACTTCGGTGCAATTCTACG
1 GCACTTCGGTGCAATTCTACG
88574 TGACACTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCA
Found at i:88650 original size:24 final size:25
Alignment explanation
Indices: 88618--88666 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 25
88608 AATCCAATCC
88618 GATCCAAAAAA-ATAACCGAAAACT
1 GATCCAAAAAACATAACCGAAAACT
88642 GATCCAAAAAACTGATAACCGAAAA
1 GATCCAAAAAAC--ATAACCGAAAA
88667 AAATTGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.50
27 11 0.50
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.12
Consensus pattern (25 bp):
GATCCAAAAAACATAACCGAAAACT
Found at i:88677 original size:16 final size:17
Alignment explanation
Indices: 88647--88679 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
88637 AAACTGATCC
88647 AAAAAACTGATAACCGA
1 AAAAAACTGATAACCGA
*
88664 AAAAAATTGA-AACCGA
1 AAAAAACTGATAACCGA
88680 TTTAGTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.15, G:0.12, T:0.12
Consensus pattern (17 bp):
AAAAAACTGATAACCGA
Found at i:90161 original size:22 final size:22
Alignment explanation
Indices: 90119--90160 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
90109 ACAGACAAGG
* *
90119 TGTGATTGAACTCAGCTAAAAC
1 TGTGATTGAACTCACCAAAAAC
90141 TGTGATTGAACT-ACCAAAAA
1 TGTGATTGAACTCACCAAAAA
90161 AGAAGTCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (22 bp):
TGTGATTGAACTCACCAAAAAC
Found at i:93218 original size:45 final size:45
Alignment explanation
Indices: 93150--93255 Score: 180
Period size: 45 Copynumber: 2.4 Consensus size: 45
93140 TCAGGAATGC
93150 TTTA-AATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
1 TTTAGAATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
*
93194 TTTAGAATTTGAACAATTGCACAACTTTTAGTAGTGTATTTGGGG
1 TTTAGAATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
93239 TTT-GAAATTTGAACAAT
1 TTTAG-AATTTGAACAAT
93256 GTGCTATTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
44 5 0.08
45 54 0.92
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (45 bp):
TTTAGAATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
Found at i:99357 original size:103 final size:103
Alignment explanation
Indices: 99173--99398 Score: 382
Period size: 103 Copynumber: 2.2 Consensus size: 103
99163 GTCGAGGGTC
99173 TATGTGGTCCTTCAGGACATATATGTATTCCTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCCTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
99238 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
99276 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCCTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
99341 TTGATCCCTAGTATATGTATATGATTCTTAATGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
99379 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
99399 TATTATATGG
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCCTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:99451 original size:47 final size:47
Alignment explanation
Indices: 99397--99516 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
99387 CCTTATGGAC
99397 ATTATTATATGGCACTACGGTGCAATTCTACGAGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGAGGCACTCCGGTGCA
** *
99444 ATTATTATATGGCACTACAATGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGAGGCACTCCGGTGCA
* *
99491 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
99517 ATATGAGCTG
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
46 18 0.27
47 48 0.73
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGAGGCACTCCGGTGCA
Found at i:99517 original size:23 final size:23
Alignment explanation
Indices: 99397--99521 Score: 115
Period size: 23 Copynumber: 5.3 Consensus size: 23
99387 CCTTATGGAC
*
99397 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
99421 ATTCTACGAGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* **
99444 ATTATTATATGGCACTACAATGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
99468 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
99491 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
99514 ATTATATG
1 ATTATATG
99522 AGCTGTGGTG
Statistics
Matches: 77, Mismatches: 23, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
23 58 0.75
24 19 0.25
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:104290 original size:23 final size:22
Alignment explanation
Indices: 104242--104290 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
104232 CCAAAATGTC
104242 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
104263 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
104286 AAGGA
1 AAGGA
104291 AAAATTGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:105211 original size:103 final size:103
Alignment explanation
Indices: 104986--105203 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
104976 GTCGAGGGTC
104986 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
105051 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
105089 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
105154 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
105192 TATGTGGTCCTT
1 TATGTGGTCCTT
105204 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:105264 original size:47 final size:47
Alignment explanation
Indices: 105210--105329 Score: 215
Period size: 47 Copynumber: 2.6 Consensus size: 47
105200 CCTTATGGAC
105210 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
105257 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
105304 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
105330 ATATGAGCTG
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
46 20 0.28
47 51 0.72
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
Found at i:105330 original size:23 final size:23
Alignment explanation
Indices: 105210--105334 Score: 133
Period size: 23 Copynumber: 5.3 Consensus size: 23
105200 CCTTATGGAC
*
105210 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
105234 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
105257 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
105281 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
105304 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
105327 ATTATATG
1 ATTATATG
105335 AGCTGTGGTG
Statistics
Matches: 81, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
23 60 0.74
24 21 0.26
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:107836 original size:20 final size:20
Alignment explanation
Indices: 107811--107850 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
107801 ATAGAATGTT
*
107811 ATAGGGGTACCGATTCCCCC
1 ATAGGGGTACCGATACCCCC
107831 ATAGGGGTACCGATACCCCC
1 ATAGGGGTACCGATACCCCC
107851 CTAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (20 bp):
ATAGGGGTACCGATACCCCC
Found at i:107862 original size:65 final size:65
Alignment explanation
Indices: 107740--107863 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 65
107730 GAAATTCCAT
* * * *
107740 AATGTTATGGGGGTACCGATTCCCCCCAGAGGGGTACCGATACCCCCTTGACAAAAAAATTATAG
1 AATGTTATAGGGGTACCGATTCCCCCCAGAGGGGTACCGATACCCCCCTAAAAAAAAAATTATAG
*
107805 AATGTTATAGGGGTACCGATT-CCCCCATAGGGGTACCGATACCCCCCTAAAAGAAAAAA
1 AATGTTATAGGGGTACCGATTCCCCCCAGAGGGGTACCGATACCCCCCTAAAA-AAAAAA
107864 ATGAAACATT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
64 27 0.51
65 26 0.49
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (65 bp):
AATGTTATAGGGGTACCGATTCCCCCCAGAGGGGTACCGATACCCCCCTAAAAAAAAAATTATAG
Found at i:113576 original size:17 final size:17
Alignment explanation
Indices: 113551--113586 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
113541 GATCTTACGC
* *
113551 TTCAGTGCCTTACAGTT
1 TTCAATGCCTTACAATT
113568 TTCAATGCCTTACAATT
1 TTCAATGCCTTACAATT
113585 TT
1 TT
113587 TAGCGGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (17 bp):
TTCAATGCCTTACAATT
Found at i:116371 original size:30 final size:30
Alignment explanation
Indices: 116254--116372 Score: 141
Period size: 30 Copynumber: 4.0 Consensus size: 30
116244 GCAATGGCCT
* *
116254 AAATAGCAAAATCAAAAATTTAAAGGACT-
1 AAATAGCAAAAACAAAAAGTTAAAGGACTA
*
116283 AAATAGCAAAAACAAAAAGTTAAAGGACCA
1 AAATAGCAAAAACAAAAAGTTAAAGGACTA
* * * *
116313 AAATAGAAAAAATAGAAACTTAAAGGACTA
1 AAATAGCAAAAACAAAAAGTTAAAGGACTA
* * *
116343 AAATAGCTAAAACATAAAGTTAATGGACTA
1 AAATAGCAAAAACAAAAAGTTAAAGGACTA
116373 CACAATAATT
Statistics
Matches: 75, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 26 0.35
30 49 0.65
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.18
Consensus pattern (30 bp):
AAATAGCAAAAACAAAAAGTTAAAGGACTA
Found at i:117234 original size:12 final size:12
Alignment explanation
Indices: 117202--117244 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
117192 CTAAGGTGAG
117202 TTTCATTTTTTTC
1 TTTC-TTTTTTTC
*
117215 TCTCTCTTTTTTTT
1 T-T-TCTTTTTTTC
117229 TTTCTTTTTTTC
1 TTTCTTTTTTTC
117241 TTTC
1 TTTC
117245 GATTTTCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 13 0.50
13 2 0.08
14 9 0.35
15 2 0.08
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:122815 original size:5 final size:5
Alignment explanation
Indices: 122805--122866 Score: 70
Period size: 5 Copynumber: 12.4 Consensus size: 5
122795 CTCGACCACA
* * * *
122805 AGCCG AGCCG AGCCG AGCCG TGCCG TGCCG AGCCG AGCCG AGACG AGACG
1 AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG
* *
122855 AGACG AGACG AG
1 AGCCG AGCCG AG
122867 ACGGACGGAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 54 1.00
ACGTcount: A:0.24, C:0.32, G:0.40, T:0.03
Consensus pattern (5 bp):
AGCCG
Found at i:122867 original size:5 final size:5
Alignment explanation
Indices: 122833--122877 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
122823 CGTGCCGTGC
* *
122833 CGAGC CGAGC CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
122878 GCGGCGGCGG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
4 8 0.21
5 31 0.79
ACGTcount: A:0.31, C:0.27, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:136039 original size:23 final size:23
Alignment explanation
Indices: 136013--136074 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
136003 ACATGTAAAA
* * *
136013 ATATGATGTAATAGGTATCGCTT
1 ATATAATGTAATAGGTAGCGATT
136036 ATATAATGTAATAGGTAGCGATT
1 ATATAATGTAATAGGTAGCGATT
**
136059 ATATAATAAAATAGGT
1 ATATAATGTAATAGGT
136075 TAATTACTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGATT
Found at i:136145 original size:22 final size:23
Alignment explanation
Indices: 136120--136183 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
136110 TTATGTACTT
136120 CTTATATAATGT-ATAGGTAGCG
1 CTTATATAATGTAATAGGTAGCG
* *
136142 CTTATATAATGTAATATGTAGTG
1 CTTATATAATGTAATAGGTAGCG
**
136165 CTTATATAATAAAATAGGT
1 CTTATATAATGTAATAGGT
136184 TAATTACTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 12 0.33
23 24 0.67
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
CTTATATAATGTAATAGGTAGCG
Found at i:136146 original size:109 final size:110
Alignment explanation
Indices: 136013--136261 Score: 383
Period size: 109 Copynumber: 2.3 Consensus size: 110
136003 ACATGTAAAA
* *
136013 ATATGATGTAATAGGTATCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAA
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAA
* * * **
136078 TTACTGGAAACATTACCAAGCACAATAACATATTATGTACTTCTT
66 TTACTAGAAACATTACCAAACACAATAACATATTAGGTACAGCTT
* * *
136123 ATATAATGT-ATAGGTAGCGCTTATATAATGTAATATGTAGTGCTTATATAATAAAATAGGTTAA
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAA
* *
136187 TTACTAGAAACATTATCAAACACAATAACATATTAGGTAGAGCTT
66 TTACTAGAAACATTACCAAACACAATAACATATTAGGTACAGCTT
136232 ATATAATGTAATAGGTAGCGCTTATATAAT
1 ATATAATGTAATAGGTAGCGCTTATATAAT
136262 AAAATAAGTT
Statistics
Matches: 126, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
109 98 0.78
110 28 0.22
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.35
Consensus pattern (110 bp):
ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAA
TTACTAGAAACATTACCAAACACAATAACATATTAGGTACAGCTT
Found at i:136167 original size:23 final size:22
Alignment explanation
Indices: 136111--136174 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 22
136101 AATAACATAT
* *
136111 TATGTACTTCTTATATAATGTA
1 TATGTAGTGCTTATATAATGTA
* *
136133 TAGGTAGCGCTTATATAATGTAA
1 TATGTAGTGCTTATATAATGT-A
136156 TATGTAGTGCTTATATAAT
1 TATGTAGTGCTTATATAAT
136175 AAAATAGGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.44
Consensus pattern (22 bp):
TATGTAGTGCTTATATAATGTA
Found at i:136232 original size:87 final size:87
Alignment explanation
Indices: 136133--136363 Score: 363
Period size: 87 Copynumber: 2.7 Consensus size: 87
136123 ATATAATGTA
* *
136133 TAGGTAGCGCTTATATAATGTAATATGTAGTGCTTATATAATAAAATAGGTTAATTACTAGAAAC
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
136198 ATTATCAAACACAATAACATAT
66 ATTATCAAACACAATAACATAT
* * *
136220 TAGGTAGAGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAAGTTAATTACTGGAAAC
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
*
136285 ATTATCAAGCACAATAACATAT
66 ATTATCAAACACAATAACATAT
* ** * *
136307 TAGATAGCGCTTATATAACATAATAGGTAACACTTATATAATAAAATAGGTTAATTA
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTA
136364 TTTAATTTGT
Statistics
Matches: 131, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 131 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (87 bp):
TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
ATTATCAAACACAATAACATAT
Found at i:136237 original size:23 final size:23
Alignment explanation
Indices: 136211--136260 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
136201 ATCAAACACA
*
136211 ATAACATATTAGGTAGAGCTTAT
1 ATAACATAATAGGTAGAGCTTAT
** *
136234 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGAGCTTAT
136257 ATAA
1 ATAA
136261 TAAAATAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTAGAGCTTAT
Found at i:136267 original size:23 final size:23
Alignment explanation
Indices: 136220--136267 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
136210 AATAACATAT
**
136220 TAGGTAGAGCTTATATAATGTAA
1 TAGGTAGAGCTTATATAATAAAA
*
136243 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGAGCTTATATAATAAAA
136266 TA
1 TA
136268 AGTTAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (23 bp):
TAGGTAGAGCTTATATAATAAAA
Found at i:136324 original size:23 final size:23
Alignment explanation
Indices: 136298--136347 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
136288 ATCAAGCACA
* * *
136298 ATAACATATTAGATAGCGCTTAT
1 ATAACATAATAGATAACACTTAT
*
136321 ATAACATAATAGGTAACACTTAT
1 ATAACATAATAGATAACACTTAT
136344 ATAA
1 ATAA
136348 TAAAATAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGATAACACTTAT
Found at i:136681 original size:14 final size:14
Alignment explanation
Indices: 136662--136706 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
136652 TATTAGAATA
*
136662 ATTTATTTAATATT
1 ATTTATTAAATATT
136676 ATTTATGTAAATATT
1 ATTTAT-TAAATATT
136691 A-TTATTAAAATATT
1 ATTTATT-AAATATT
136705 AT
1 AT
136707 ATCTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 18 0.67
15 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:136720 original size:28 final size:28
Alignment explanation
Indices: 136634--136757 Score: 81
Period size: 28 Copynumber: 4.7 Consensus size: 28
136624 TAACAAAATA
*
136634 ATAATATTATTTTTAAAATATTA-GA--
1 ATAATATTATTATTAAAATATTATGATT
*
136659 ATAAT-TTA-T-TT--AATATTATTTATGT
1 ATAATATTATTATTAAAATATTA-TGAT-T
136684 A-AATATTATTATTAAAATATTAT-ATCT
1 ATAATATTATTATTAAAATATTATGAT-T
* * * *
136711 ATAATTTTATAAATAAAAAATTATGATT
1 ATAATATTATTATTAAAATATTATGATT
*
136739 ATTATATT-TTATTAAAATA
1 ATAATATTATTATTAAAATA
136758 AAATTATTAT
Statistics
Matches: 76, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.09
22 3 0.04
23 1 0.01
24 6 0.08
25 9 0.12
26 1 0.01
27 14 0.18
28 26 0.34
29 9 0.12
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (28 bp):
ATAATATTATTATTAAAATATTATGATT
Found at i:137397 original size:24 final size:25
Alignment explanation
Indices: 137370--137438 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
137360 AACATCAAAT
137370 ACAATAA-AATAATATTATTTATTA
1 ACAATAAGAATAATATTATTTATTA
*
137394 ACAA-AATAATAATATTATTT-TTA
1 ACAATAAGAATAATATTATTTATTA
137417 A-AATATTAGAATAAT-TTATTTA
1 ACAATA--AGAATAATATTATTTA
137439 ATATTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 23 0.59
25 7 0.18
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
ACAATAAGAATAATATTATTTATTA
Found at i:138111 original size:198 final size:198
Alignment explanation
Indices: 137651--138319 Score: 956
Period size: 198 Copynumber: 3.4 Consensus size: 198
137641 CACATATGTT
* * *
137651 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGT-ACCGATAGAAATATACCGG
* * ***
137716 TTTTATGAGAGAATATG-TCTACATAATGTATCGACACAAATTTAA-AAAGTGTCGATACATTTT
65 TTTTATGAGAAAATA-GATCTACATAATGTATCGACAC-ATTTTAAGTTTGTGTCGATAC-TTTT
* * *
137779 GTCCAGAATGAATG-CCAAATGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGA
127 TTCCAGAATGAATGTCC-AACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATTGA
137843 TCCCAAAA
191 TCCCAAAA
* *
137851 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACTCGGTAGAAATATATCGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAC-CGATAGAAATATACCGG
* *
137916 TTTTATGAGAAAATAGATATGCATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
65 TTTTATGAGAAAATAGATCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
* *
137981 CAGAAAGAATGTCCAACGAGGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATTGATCCC
130 CAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATTGATCCC
138046 AAAA
195 AAAA
* * *
138050 A-TTCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCTGGTAGAAATATATCGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACC-GATAGAAATATACCGG
* *
138114 TTTTATGAGAAAATA-AGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTAGATACTTTTTT
65 TTTTATGAGAAAATAGA-TCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTT
*
138178 CCAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA--AAATTGTATTGATC
129 CCAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATTGATC
138241 CCAAAA
193 CCAAAA
* ** *
138247 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTGTAATGTTACCGATATAAATATACCGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATG-TACCGATAGAAATATACCGG
138312 TTTTATGA
65 TTTTATGA
138320 TAGAATAAGT
Statistics
Matches: 428, Mismatches: 32, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
196 3 0.01
197 18 0.04
198 224 0.52
199 82 0.19
200 101 0.24
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (198 bp):
ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCGATAGAAATATACCGGT
TTTATGAGAAAATAGATCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTCC
AGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATTGATCCCA
AAA
Found at i:138446 original size:87 final size:87
Alignment explanation
Indices: 138332--138570 Score: 352
Period size: 87 Copynumber: 2.7 Consensus size: 87
138322 GAATAAGTTA
* * *
138332 ATATAAGCGCTGCATATTGCATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACATATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTT
138397 TCAGTAATTAACCTATTTTATT
66 TCAGTAATTAACCTATTTTATT
* * * * *
138419 ATATCAGCGCTACCTATTACATTATATAAACGCAACCTAATATGTTATTGTGTTTGATAATGTTT
1 ATATAAGCGCTACATATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTT
138484 TCAGTAATTAACCTATTTTATT
66 TCAGTAATTAACCTATTTTATT
* * * * * *
138506 ATATAAGCGCTACATATTACATTATATAAACGCTACATAATTTATTATTTTACTTAATAATATTT
1 ATATAAGCGCTACATATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTT
138571 CCGGTTAAAT
Statistics
Matches: 133, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 133 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTACATATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTT
TCAGTAATTAACCTATTTTATT
Found at i:138456 original size:23 final size:23
Alignment explanation
Indices: 138406--138457 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
138396 TTCAGTAATT
** * *
138406 AACCTATTTTATTATATCAGCGC
1 AACCTATTACATTATATAAACGC
*
138429 TACCTATTACATTATATAAACGC
1 AACCTATTACATTATATAAACGC
138452 AACCTA
1 AACCTA
138458 ATATGTTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.35
Consensus pattern (23 bp):
AACCTATTACATTATATAAACGC
Found at i:138552 original size:23 final size:22
Alignment explanation
Indices: 138500--138553 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
138490 ATTAACCTAT
*
138500 TTTATTATATAAGCGCTACATA
1 TTTATTATATAAACGCTACATA
*
138522 TTACATTATATAAACGCTACATAA
1 TT-TATTATATAAACGCTACAT-A
138546 TTTATTAT
1 TTTATTAT
138554 TTTACTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 22 0.81
24 3 0.11
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.43
Consensus pattern (22 bp):
TTTATTATATAAACGCTACATA
Found at i:139536 original size:19 final size:20
Alignment explanation
Indices: 139512--139562 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
139502 AATGACCAAT
139512 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
139531 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
139551 AAAATCGCAACG
1 AAAATCGCAACG
139563 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:139556 original size:20 final size:20
Alignment explanation
Indices: 139512--139789 Score: 139
Period size: 20 Copynumber: 13.6 Consensus size: 20
139502 AATGACCAAT
* *
139512 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
139531 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
139551 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
139571 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
139591 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
139612 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
139635 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
139655 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
139675 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
139695 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
139715 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * * *
139738 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* *
139758 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
139778 AAAATCGCAACG
1 AAAATCGCAACG
139790 GTCAAAAGAA
Statistics
Matches: 205, Mismatches: 42, Indels: 23
0.76 0.16 0.09
Matches are distributed among these distances:
19 17 0.08
20 144 0.70
21 15 0.07
22 1 0.00
23 28 0.14
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:139723 original size:63 final size:63
Alignment explanation
Indices: 139656--139779 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
139646 GCGATTGATT
* * * * * *
139656 GAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGA
1 GAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTGAGAAGA
139719 GAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTGAGAA
1 GAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTGAGAA
139780 AATCGCAACG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (63 bp):
GAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTGAGAAGA
Found at i:139727 original size:83 final size:83
Alignment explanation
Indices: 139616--139789 Score: 258
Period size: 83 Copynumber: 2.1 Consensus size: 83
139606 GCTTCCAAGT
* ** * * *
139616 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* * *
139681 GCAATGCGATTGAGAGAG
66 GCAACGCGATTGAGAAAA
*
139699 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
139764 GCAACGCGATTGAGAAAA
66 GCAACGCGATTGAGAAAA
139782 TCGCAACG
1 TCGCAACG
139790 GTCAAAAGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAACGCGATTGAGAAAA
Found at i:139778 original size:40 final size:40
Alignment explanation
Indices: 139637--139787 Score: 185
Period size: 40 Copynumber: 3.7 Consensus size: 40
139627 TTTAGAAGAA
** * *
139637 AATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* *
139677 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGA-TT-G-AGAG
* *
139720 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* *
139760 AATCGCAACGCGATTGAGAAAATCGCAA
1 AATCGCAATGCGATTGAGAGAATCGCAA
139788 CGGTCAAAAG
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
40 58 0.61
41 3 0.03
42 1 0.01
43 33 0.35
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
Found at i:139916 original size:15 final size:15
Alignment explanation
Indices: 139879--139930 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
139869 CACGTATTAC
139879 CACGACCACGACCACGA
1 CACGACC-CGACC-CGA
139896 CACGACCCGACCCGA
1 CACGACCCGACCCGA
*
139911 CCCGACCCGACCCGA
1 CACGACCCGACCCGA
*
139926 GACGA
1 CACGA
139931 GACGGCGGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 20 0.62
16 5 0.16
17 7 0.22
ACGTcount: A:0.29, C:0.50, G:0.21, T:0.00
Consensus pattern (15 bp):
CACGACCCGACCCGA
Found at i:139922 original size:5 final size:5
Alignment explanation
Indices: 139881--139925 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
139871 CGTATTACCA
*
139881 CGACC ACGACC ACGACA CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGA
139926 GACGAGACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
5 27 0.73
6 10 0.27
ACGTcount: A:0.27, C:0.53, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:140657 original size:6 final size:6
Alignment explanation
Indices: 140615--140735 Score: 155
Period size: 6 Copynumber: 20.5 Consensus size: 6
140605 TCTCGTCTCG
140615 GGTCG- GGTCG- GGTCG- GGTCGT -GTCGT -GTCGT -GTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
140657 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
*
140705 GGTAATACGT GTTCGT GGTCGT GGTCGT GGT
1 GG---T-CGT GGTCGT GGTCGT GGTCGT GGT
140736 AATACGTGTC
Statistics
Matches: 108, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
5 30 0.28
6 72 0.67
7 1 0.01
9 1 0.01
10 4 0.04
ACGTcount: A:0.02, C:0.17, G:0.48, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:140812 original size:19 final size:20
Alignment explanation
Indices: 140774--140822 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
140764 ATACTATCTT
*
140774 TTGCGATTTTCTAAATCGCG
1 TTGCGATTTTCGAAATCGCG
*
140794 TTGCGATTTT-GATATCGCG
1 TTGCGATTTTCGAAATCGCG
140813 TTGCGATTTT
1 TTGCGATTTT
140823 ATTGGTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGATTTTCGAAATCGCG
Found at i:148314 original size:17 final size:17
Alignment explanation
Indices: 148292--148332 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
148282 GATAGCATGA
148292 CCGGTTCGCTAACCGAT
1 CCGGTTCGCTAACCGAT
*
148309 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGAT
148326 CCGGTTC
1 CCGGTTC
148333 TGAAAACCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.37, G:0.27, T:0.24
Consensus pattern (17 bp):
CCGGTTCGCTAACCGAT
Found at i:154828 original size:6 final size:6
Alignment explanation
Indices: 154817--154950 Score: 52
Period size: 6 Copynumber: 22.0 Consensus size: 6
154807 TAATCTTTTA
154817 ATTATT ATTATT ATT-TT ATATATT ACGTTA-T ATTA-T ATATATT ATTATT
1 ATTATT ATTATT ATTATT AT-TATT A--TTATT ATTATT AT-TATT ATTATT
* * * *
154866 ATATATAT ATATATT ACCTATT -TTCTT -TT-TT A-TACTC ATTACT ATT-TCT
1 AT-TAT-T AT-TATT A-TTATT ATTATT ATTATT ATTA-TT ATTATT ATTAT-T
* *
154915 ATTATT CTTATT ATT-TT CATTATT ACTATT ATTATT
1 ATTATT ATTATT ATTATT -ATTATT ATTATT ATTATT
154951 GTTTTGTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
4 3 0.03
5 17 0.17
6 48 0.48
7 22 0.22
8 9 0.09
9 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.60
Consensus pattern (6 bp):
ATTATT
Found at i:154829 original size:9 final size:9
Alignment explanation
Indices: 154817--154950 Score: 52
Period size: 9 Copynumber: 14.7 Consensus size: 9
154807 TAATCTTTTA
154817 ATTATTATT
1 ATTATTATT
154826 ATTATT-TT
1 ATTATTATT
154834 ATATATTACGTT
1 AT-TATTA--TT
154846 A-TATTA-T
1 ATTATTATT
154853 ATATATTATT
1 AT-TATTATT
154863 ATTATATATAT
1 ATTAT-TAT-T
*
154874 ATATATTACCT
1 AT-TATTA-TT
*
154885 ATT-TTCTT
1 ATTATTATT
154893 -TT-TTA-T
1 ATTATTATT
* *
154899 ACTCATTACT
1 A-TTATTATT
154909 ATT-TCTATT
1 ATTAT-TATT
*
154918 ATTCTTATT
1 ATTATTATT
154927 ATT-TTCATT
1 ATTATT-ATT
*
154936 ATTACTATT
1 ATTATTATT
154945 ATTATT
1 ATTATT
154951 GTTTTGTTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 38
0.67 0.06 0.26
Matches are distributed among these distances:
6 1 0.01
7 6 0.06
8 9 0.09
9 51 0.53
10 16 0.16
11 8 0.08
12 6 0.06
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.60
Consensus pattern (9 bp):
ATTATTATT
Found at i:154855 original size:19 final size:19
Alignment explanation
Indices: 154823--154882 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
154813 TTTAATTATT
*
154823 ATTATTATTTTATATATTAC
1 ATTA-TATTATATATATTAC
* *
154843 GTTATATTATATATATTATT
1 ATTATATTATATATATTA-C
154863 ATTATATATATATATATTAC
1 ATTATAT-TATATATATTAC
154883 CTATTTTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 13 0.39
20 9 0.27
21 11 0.33
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTATATTATATATATTAC
Found at i:154864 original size:17 final size:17
Alignment explanation
Indices: 154819--154881 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
154809 ATCTTTTAAT
*
154819 TATTATTATTATTTTATA
1 TATTATTA-TATTATATA
154837 TATTACGTTATATTATATA
1 TATTA--TTATATTATATA
154856 TATTATTAT-TATATATA
1 TATTATTATAT-TATATA
154873 TATATATTA
1 TAT-TATTA
154882 CCTATTTTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 1 0.03
17 13 0.32
18 10 0.25
19 13 0.32
20 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
TATTATTATATTATATA
Found at i:154880 original size:15 final size:14
Alignment explanation
Indices: 154825--154881 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 14
154815 TAATTATTAT
*
154825 TATTATTTTATATA
1 TATTATATTATATA
154839 TTACGTTATATTATATA
1 -TA--TTATATTATATA
154856 TATTATTATTATATA
1 TATTA-TATTATATA
154871 TATATATATTA
1 TAT-TATATTA
154882 CCTATTTTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 3 0.08
15 19 0.51
16 4 0.11
17 11 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (14 bp):
TATTATATTATATA
Found at i:155076 original size:17 final size:17
Alignment explanation
Indices: 155051--155097 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
155041 TTCTTTTCCT
155051 TTTATTTTATTTTTTTTC
1 TTTA-TTTATTTTTTTTC
* *
155069 TTTATTTATTATTTTTG
1 TTTATTTATTTTTTTTC
*
155086 TATA-TTATTTTT
1 TTTATTTATTTTT
155098 ATTTATCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 7 0.28
17 14 0.56
18 4 0.16
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTATTTATTTTTTTTC
Found at i:157133 original size:23 final size:23
Alignment explanation
Indices: 157115--157175 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
157105 CTCGTATAAC
157115 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
157138 TGTACCGGAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
157161 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
157176 TAGAATACTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:157370 original size:103 final size:104
Alignment explanation
Indices: 157191--157405 Score: 369
Period size: 103 Copynumber: 2.1 Consensus size: 104
157181 TACTGTCCAT
* * * *
157191 AAGGACTACATATCATTCCTTAAGAATCATATATATATATACTAGGGATCAAGTATGTGTCTCAC
1 AAGGACCACATATCATTCCTTAAGAATCA-ATATACATATACCAAGGATCAAGTATGTGTCTCAC
157256 CAGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 CAGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
157296 AAGGACCACATATCATTCCTTAAGAATC-ATATACATATGCCAAGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCAATATACATATACCAAGGATCAAGTATGTGTCTCACC
157360 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
157399 AAGGACC
1 AAGGACC
157406 GCGTAGACCC
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 78 0.74
105 27 0.26
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (104 bp):
AAGGACCACATATCATTCCTTAAGAATCAATATACATATACCAAGGATCAAGTATGTGTCTCACC
AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:159113 original size:21 final size:21
Alignment explanation
Indices: 159089--159133 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
159079 TTTTGTTCGT
* *
159089 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
159110 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
159131 TTG
1 TTG
159134 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:161372 original size:312 final size:312
Alignment explanation
Indices: 160807--162043 Score: 2366
Period size: 312 Copynumber: 4.0 Consensus size: 312
160797 AGTCTACGTC
160807 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
160872 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
*
160937 GAGAACAATACAAATTTGTAAACTTATAAGGAAATCCTCACAAGATAGATTGTTTGCACAATTCT
131 GAGAACAATACAAATTTGTAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
* *
161002 AGAACAAAGAAACGAACACCCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
196 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
161067 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
261 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
161119 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
161184 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
*
161249 GAGAACAATACAAATTTGCAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
131 GAGAACAATACAAATTTGTAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
161314 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
196 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
161379 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
261 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
*
161431 CACTATCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
* *
161496 CAAAGAGTAACCTTACAAACCATCAAGAAATATACCCCAAATTCTTGAGAACACTCTCTCCCAGA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
161561 GAGAACAATACAAATTTGTAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
131 GAGAACAATACAAATTTGTAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
161626 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
196 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
*
161691 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAATTTAGGATTTTCCA
261 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
161743 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
1 CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
161808 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
66 CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
*
161873 GAGAACAATACAAATTTGAAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
131 GAGAACAATACAAATTTGTAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
*
161938 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGTACAATAAGTGTTCTTGAAAGCAAA
196 AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
* *
162003 ATGAATAATGAATGAAAAATAGGATTGAAATGCTCAAACTT
261 ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTT
162044 GAGGTTTGAT
Statistics
Matches: 908, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
312 908 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (312 bp):
CACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGA
CAAAGAGTAACCTTACAAACCATCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCAAA
GAGAACAATACAAATTTGTAAACTTATAAGGAAATCCTCACAAGGTAGATTGTTTGCACAATTCT
AGAACAAAGAAAAGAACACTCAAGAATGAATACAATTGAGCACAATAAGTGTTCTTGAAAGCAAA
ATGAATATTGAATGAAAAATAGGCTTGAAATGCTCAAACTTAGGATTTTCCA
Found at i:166028 original size:36 final size:36
Alignment explanation
Indices: 165981--166059 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
165971 ATAGACTTTG
165981 TCTCACTTGAGACTGCTTTACTCGAAAGAAGATTTA
1 TCTCACTTGAGACTGCTTTACTCGAAAGAAGATTTA
* * * *
166017 TCTCACTTGAGATTGTTTTATTCGAAAGAATATTTA
1 TCTCACTTGAGACTGCTTTACTCGAAAGAAGATTTA
*
166053 TTTCACT
1 TCTCACT
166060 CAAGATTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (36 bp):
TCTCACTTGAGACTGCTTTACTCGAAAGAAGATTTA
Found at i:166066 original size:36 final size:36
Alignment explanation
Indices: 165997--166071 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
165987 TTGAGACTGC
**
165997 TTTACTCGAAAGAAGATTTATCTCACTTGAGATTGT
1 TTTACTCGAAAGAAGATTTATCTCACTCAAGATTGT
* * *
166033 TTTATTCGAAAGAATATTTATTTCACTCAAGATTGT
1 TTTACTCGAAAGAAGATTTATCTCACTCAAGATTGT
166069 TTT
1 TTT
166072 TCTTAAAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (36 bp):
TTTACTCGAAAGAAGATTTATCTCACTCAAGATTGT
Found at i:166334 original size:65 final size:65
Alignment explanation
Indices: 166206--166386 Score: 258
Period size: 65 Copynumber: 2.8 Consensus size: 65
166196 CTTGAGATAG
* *
166206 TTTCCCTTGAACCA-GAATTTTGTC-CCTCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAA
1 TTTCCCTTGAA--ATGAATTTTGTCTCCT-TTGAGACAGTTTCTCTTGAAACATAAACATCGAAA
166269 ACA
63 ACA
* *
166272 TTTCTCTTGAAATGGATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAACA
* * *
166337 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACA
166387 AAATTTTGTC
Statistics
Matches: 104, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
64 1 0.01
65 90 0.87
66 13 0.12
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (65 bp):
TTTCCCTTGAAATGAATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAACA
Found at i:166399 original size:37 final size:37
Alignment explanation
Indices: 166337--166423 Score: 131
Period size: 37 Copynumber: 2.4 Consensus size: 37
166327 ATCGAAAACA
** *
166337 TTTCCCTTGAAA-TGAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
166373 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
166410 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
166424 TAAACATTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 12 0.26
37 34 0.74
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:166405 original size:102 final size:102
Alignment explanation
Indices: 166287--166492 Score: 358
Period size: 102 Copynumber: 2.0 Consensus size: 102
166277 CTTGAAATGG
* **
166287 ATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAACATTTCCCTTGAAATGA
1 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAACATTTCCCTTGAAACAA
*
166352 ATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAA
66 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
*
166389 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAACATTTCCCTTGAAACAA
*
166454 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
66 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
166491 AT
1 AT
166493 CTTTTAATCT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (102 bp):
ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAACATTTCCCTTGAAACAA
ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:166472 original size:167 final size:167
Alignment explanation
Indices: 166167--166662 Score: 500
Period size: 167 Copynumber: 2.9 Consensus size: 167
166157 CTTGAGGTGG
* * * * *
166167 TTTCCCTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAACCAGAATTTTGTC-C
1 TTTCCCTTGAAAC--AA-ATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
* * ***
166231 CTCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAACATTTCTCTTGAAATGGATTTTGTCT
63 C-CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAAAAATTTTGTCT
166296 CCTTTGAGACAGTTTCTCTTGAAACATAAA-CATCGAAAAC-A
127 CC-TTGAGACAGTTTCTCTTGAAACATAAATC-TCGAAAACTA
**
166337 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
166402 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAACAAATTTTGTCTCTCT
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAAAAATTTTGTCTC-CT
* *** * *
166467 TGAGACAGTTTCCCTTGAAACA-AAATCTTTTAATCTG
130 TGAGACAGTTTCTCTTGAAACATAAATCTCGAAAACTA
* * * * * ** *
166504 TTTTCCTTTAAACAAATTTTGTCTCTCTCGAGACAGTTTCTTTTGAAAC-AAATTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * * * *** * *
166568 TGAGATAG-TTCCCTTGAAACACAAAATCTTTGAATTTATTTCCCTTAAAATAAAATTTTGTTTA
66 TGAGACAGTTTCTCTTGAAACA-TAAA-CATTGAAAACATTTCCCTTGAAA-AAAATTTTGTCT-
* *
166632 CCTTGAGACCGTTTCTCATGAAACAATAAAT
127 CCTTGAGACAGTTTCTCTTGAAAC-ATAAAT
166663 ATCTTTGAGA
Statistics
Matches: 275, Mismatches: 41, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
165 12 0.04
166 31 0.11
167 181 0.66
168 34 0.12
169 2 0.01
170 15 0.05
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (167 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAAAAATTTTGTCTCCTT
GAGACAGTTTCTCTTGAAACATAAATCTCGAAAACTA
Found at i:166478 original size:65 final size:65
Alignment explanation
Indices: 166373--166555 Score: 235
Period size: 65 Copynumber: 2.8 Consensus size: 65
166363 CTTGAGATAG
*
166373 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAA
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAATC-TTGAAAA
166437 C-A
63 CTA
* ** * *
166439 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTTAATCTG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTGAAAACTA
* * * *
166504 TTTTCCTTTAAACAAATTTTGTCTCTCTCGAGACAGTTTCTTTTGAAACAAA
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
166556 TTTTGTCTCT
Statistics
Matches: 104, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
64 8 0.08
65 83 0.80
66 13 0.12
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (65 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTGAAAACTA
Found at i:166486 original size:36 final size:36
Alignment explanation
Indices: 166439--166588 Score: 156
Period size: 36 Copynumber: 4.4 Consensus size: 36
166429 ATTGAAAACA
166439 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
166475 TTTCCCTTGAAACAAA----ATCT-T-TT-A-ATCTG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-CAG
* * *
166504 TTTTCCTTTAAACAAATTTTGTCTCTCTCGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
** *
166540 TTTCTTTTGAAACAAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
166576 -TTCCCTTGAAACA
1 TTTCCCTTGAAACA
166589 CAAAATCTTT
Statistics
Matches: 90, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
28 1 0.01
29 17 0.19
30 2 0.02
31 1 0.01
32 3 0.03
33 3 0.03
34 1 0.01
35 12 0.13
36 49 0.54
37 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:168106 original size:18 final size:19
Alignment explanation
Indices: 168080--168117 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
168070 TGGAGTTCTA
168080 TTTCTATTATT-CTTATTAT
1 TTTCTATTATTAC-TATTAT
168099 TTTC-ATTATTACTATTAT
1 TTTCTATTATTACTATTAT
168117 T
1 T
168118 ATTGTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTCTATTATTACTATTAT
Found at i:168150 original size:8 final size:8
Alignment explanation
Indices: 168139--168165 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
168129 TTTACTTATT
168139 TATGTATA
1 TATGTATA
168147 TATGTATA
1 TATGTATA
168155 TATGTATA
1 TATGTATA
168163 TAT
1 TAT
168166 TTTTACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (8 bp):
TATGTATA
Found at i:168262 original size:13 final size:13
Alignment explanation
Indices: 168233--168278 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
168223 TTTCCTTTCC
168233 TTTTATTT-TT-T
1 TTTTATTTATTAT
168244 TCTTTATTTATTAT
1 T-TTTATTTATTAT
*
168258 TTTTATATATTAT
1 TTTTATTTATTAT
168271 TTTTATTT
1 TTTTATTT
168279 CTCATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 1 0.03
12 7 0.23
13 20 0.67
14 2 0.07
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTATTAT
Found at i:168285 original size:20 final size:20
Alignment explanation
Indices: 168247--168285 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
168237 ATTTTTTTCT
*
168247 TTATTTATTATTTTTATATA
1 TTATTTATTATTTTCATATA
168267 TTATTT-TTATTTCTCATAT
1 TTATTTATTATTT-TCATAT
168286 TTTTAGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATTTATTATTTTCATATA
Found at i:169338 original size:6 final size:6
Alignment explanation
Indices: 169327--169367 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
169317 GCCTTTTGCA
169327 TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TCCAA
1 TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TCCAA
169368 AGCCATGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (6 bp):
TCCAAT
Found at i:170361 original size:12 final size:12
Alignment explanation
Indices: 170344--170378 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
170334 AAGAACACCA
170344 AAAGAAAAACTT
1 AAAGAAAAACTT
170356 AAAG-AAAACTT
1 AAAGAAAAACTT
*
170367 AATGAAAAACTT
1 AAAGAAAAACTT
170379 GATGTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (12 bp):
AAAGAAAAACTT
Found at i:181118 original size:29 final size:29
Alignment explanation
Indices: 181055--181159 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 29
181045 ACAGTCAACT
* * * *
181055 ATTACGAAAATAACACATTTCTTAAAAATA
1 ATTACCAAAATATCACCTTT-TTCAAAATA
181085 ATTACCAAAATATCACCTTTTTCAAAATA
1 ATTACCAAAATATCACCTTTTTCAAAATA
* * **
181114 ATTACCATAATATCATCGATTTCAAAATA
1 ATTACCAAAATATCACCTTTTTCAAAATA
*
181143 ATTACTAAAATATCACC
1 ATTACCAAAATATCACC
181160 GGGTCGGGTC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
29 47 0.73
30 17 0.27
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (29 bp):
ATTACCAAAATATCACCTTTTTCAAAATA
Done.