Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3556
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: 38428
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Found at i:6216 original size:40 final size:40
Alignment explanation
Indices: 6025--6209 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
6015 TCGAATGATG
* * * * *
6025 TCCGGGCTAAATCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
6065 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
6105 TCTGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6144 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
6185 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6210 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 33 0.27
40 79 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:6231 original size:79 final size:79
Alignment explanation
Indices: 6078--6232 Score: 190
Period size: 79 Copynumber: 2.0 Consensus size: 79
6068 GGACTAAGAT
* * **
6078 CCGAAGGCATTTGTGCGAGATACTAATTCTGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
6143 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
6157 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
6220 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
6233 ATTCCAACGG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.60
80 24 0.37
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:27684 original size:27 final size:27
Alignment explanation
Indices: 27653--28117 Score: 158
Period size: 27 Copynumber: 17.7 Consensus size: 27
27643 TTAGTTTACC
* *
27653 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACTCAAATACCCTCGATTTGTA
* *
27680 AAATTAC-CAAAGTACCCCCGATTTATA
1 AAATTACTCAAA-TACCCTCGATTTGTA
* ***
27707 AAATTACCCAAATTTACTCGATTTGTA
1 AAATTACTCAAATACCCTCGATTTGTA
* *
27734 AAATTACTGAAATA----AGA----TA
1 AAATTACTCAAATACCCTCGATTTGTA
* ** **
27753 GAATTAC-CATTTTACCCTCGATTTACA
1 AAATTACTCA-AATACCCTCGATTTGTA
* * * **
27780 AAATTACTGAAATACCCTTGGTTTACA
1 AAATTACTCAAATACCCTCGATTTGTA
* * ***
27807 AAATTACCCAAATACCCTCTATCAATA
1 AAATTACTCAAATACCCTCGATTTGTA
*
27834 AAATTAC-CAAAATACCC-CTGGTTTGTA
1 AAATTACTC-AAATACCCTC-GATTTGTA
* * * *
27861 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACTCAAATACCCTCGATTTGTA
* *
27888 AAATAAC-CAAAATACCC-CTGGTTTGT-
1 AAATTACTC-AAATACCCTC-GATTTGTA
* * * *
27914 AAATTACTAAAATACCCT-GGTATATA
1 AAATTACTCAAATACCCTCGATTTGTA
*
27940 AAATCAC-CAAATACCC-C-AGTTTGTA
1 AAATTACTCAAATACCCTCGA-TTTGTA
* *
27965 AAATTAC-CAAAATATCCTTCG-TTTATA
1 AAATTACTC-AAATA-CCCTCGATTTGTA
* *
27992 AAATCAC-CAAAATACTCCT-GGTTTGTA
1 AAATTACTC-AAATAC-CCTCGATTTGTA
* * * **
28019 AAATTACTAAAATACCCTTGGTTTACA
1 AAATTACTCAAATACCCTCGATTTGTA
*
28046 AAATTAC-CAAAATACCC-CTAATTTGTA
1 AAATTACTC-AAATACCCTC-GATTTGTA
*
28073 AAATTAC-CAAAATACCC-CTGATTTGTG
1 AAATTACTC-AAATACCCTC-GATTTGTA
28100 AAATTAC-CGAAATACCCT
1 AAATTACTC-AAATACCCT
28118 TGTAGGGTAG
Statistics
Matches: 331, Mismatches: 73, Indels: 67
0.70 0.15 0.14
Matches are distributed among these distances:
18 1 0.00
19 10 0.03
23 4 0.01
25 24 0.07
26 35 0.11
27 251 0.76
28 6 0.02
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACTCAAATACCCTCGATTTGTA
Found at i:27823 original size:54 final size:54
Alignment explanation
Indices: 27765--28116 Score: 365
Period size: 54 Copynumber: 6.6 Consensus size: 54
27755 ATTACCATTT
* ** * ** *
27765 TACCCTCGATTTACAAAATTACTGAAATACCCTTGGTTTACAAAATTACCCAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
* ** *
27819 TACCCTCTATCAATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
* * * *
27873 TACCCTTGGTTTATAAAATAACCAAAATACCCCTGGTTTGT-AAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
* * * *
27926 TACCCT-GGTATATAAAATCACC-AAATACCCC-AGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
* * * *
27977 TATCCTTCG-TTTATAAAATCACCAAAATACTCCTGGTTTGTAAAATTACTAAAA
1 TA-CCCTCGATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
* * * **
28031 TACCCTTGGTTTACAAAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
* * *
28085 TACCC-CTGATTTGTGAAATTACCGAAATACCC
1 TACCCTC-GATTTATAAAATTACCAAAATACCC
28117 TTGTAGGGTA
Statistics
Matches: 251, Mismatches: 40, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
50 6 0.02
51 22 0.09
52 30 0.12
53 31 0.12
54 162 0.65
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (54 bp):
TACCCTCGATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
Found at i:28131 original size:27 final size:27
Alignment explanation
Indices: 28101--28537 Score: 549
Period size: 27 Copynumber: 16.3 Consensus size: 27
28091 TGATTTGTGA
*
28101 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
28128 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28155 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28182 AATTACCAAGAATA-TCCTGTAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
*
28209 AATTACAG-AATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
28235 AATTATCGCAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28262 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
28289 AATTACC-AGAATACCCCTGTAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
*
28316 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28343 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
28370 AATTACTGGAATACCCCTGTATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28397 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
28424 AATTACCTAAATACCCTTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28451 AAATATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
28478 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
28505 AATTACTGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
28531 AATTACC
1 AATTACC
28538 ATTTTGCCCC
Statistics
Matches: 354, Mismatches: 51, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
25 4 0.01
26 35 0.10
27 310 0.88
28 5 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:30974 original size:25 final size:24
Alignment explanation
Indices: 30918--31001 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 24
30908 TTAGTTTACC
* *
30918 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTAC--AAATACCC-CGATTTATA
30945 AAATTACAAAGTACCCCGATTTATA
1 AAATTACAAA-TACCCCGATTTATA
* *
30970 AAATTATCAAATATCTCGATTTATA
1 AAATTA-CAAATACCCCGATTTATA
30995 AAATTAC
1 AAATTAC
31002 TGAAATAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
24 1 0.02
25 34 0.67
26 9 0.18
27 7 0.14
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (24 bp):
AAATTACAAATACCCCGATTTATA
Found at i:31069 original size:26 final size:26
Alignment explanation
Indices: 31013--31071 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
31003 GAAATAAGAT
*
31013 AGAATTA-CATTTTAACCCGATTTAC
1 AGAATTACCATTTTAACCCAATTTAC
*
31038 AGAATTACCATTTTACCCTCAATTTAC
1 AGAATTACCATTTTAACC-CAATTTAC
31065 A-AATTAC
1 AGAATTAC
31072 TGAAATACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 7 0.23
26 15 0.50
27 8 0.27
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (26 bp):
AGAATTACCATTTTAACCCAATTTAC
Found at i:31245 original size:52 final size:51
Alignment explanation
Indices: 31116--31314 Score: 182
Period size: 52 Copynumber: 3.9 Consensus size: 51
31106 AAACTCGATA
*
31116 AAAAATTACCAAAATACCCTTACTTTGTAAACATT-C-CTAAAATACCTGG-TT
1 AAAAATTACCAAAATACCCTGA-TTTGTAAA-ATTACAC-AAAATACCTGGTTT
* *
31167 AATAA-TACCAAAATACCCCTGGTTTGTAAAATTACAC-AAATACCATGGCTTAT
1 AAAAATTACCAAAATA-CCCTGATTTGTAAAATTACACAAAATACC-TGG-TT-T
*
31220 AAAAATTACCAAAAT-CCCTGATTTGTAAAATTA-ACAAAATATCTTGGTTT
1 AAAAATTACCAAAATACCCTGATTTGTAAAATTACACAAAATA-CCTGGTTT
* * *
31270 ACAAAACTACCAAAA-CCCCTCGTTTTGTAAAATTAC-CAAAATACC
1 A-AAAATTACCAAAATACCCT-GATTTGTAAAATTACACAAAATACC
31315 CTAATTTGTG
Statistics
Matches: 125, Mismatches: 9, Indels: 28
0.77 0.06 0.17
Matches are distributed among these distances:
49 10 0.08
50 24 0.19
51 30 0.24
52 46 0.37
53 6 0.05
54 9 0.07
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (51 bp):
AAAAATTACCAAAATACCCTGATTTGTAAAATTACACAAAATACCTGGTTT
Found at i:31257 original size:25 final size:26
Alignment explanation
Indices: 31117--31332 Score: 135
Period size: 26 Copynumber: 8.3 Consensus size: 26
31107 AACTCGATAA
*
31117 AAAATTACCAAAATACCCTTACTTTGT
1 AAAATTACCAAAATACCCTGA-TTTGT
*
31144 AAACATT-CCTAAAATA-CCTG--GT-T
1 AAA-ATTACC-AAAATACCCTGATTTGT
*
31167 AATAA-TACCAAAATACCCCTGGTTTGT
1 AA-AATTACCAAAATA-CCCTGATTTGT
* ** *
31194 AAAATTA-CACAAATACCATGGCTTAT
1 AAAATTACCA-AAATACCCTGATTTGT
31220 AAAAATTACCAAAAT-CCCTGATTTGT
1 -AAAATTACCAAAATACCCTGATTTGT
* * * * **
31246 AAAATTAACAAAATATCTTGGTTTAC
1 AAAATTACCAAAATACCCTGATTTGT
* * *
31272 AAAACTACCAAAA-CCCCTCGTTTTGT
1 AAAATTACCAAAATACCCT-GATTTGT
*
31298 AAAATTACCAAAATACCCTAATTTGT
1 AAAATTACCAAAATACCCTGATTTGT
*
31324 GAAATTACC
1 AAAATTACC
31333 GAATACCTTG
Statistics
Matches: 144, Mismatches: 29, Indels: 33
0.70 0.14 0.16
Matches are distributed among these distances:
22 7 0.05
23 6 0.04
24 6 0.04
25 15 0.10
26 66 0.46
27 33 0.23
28 11 0.08
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (26 bp):
AAAATTACCAAAATACCCTGATTTGT
Found at i:31354 original size:25 final size:25
Alignment explanation
Indices: 31326--31830 Score: 423
Period size: 26 Copynumber: 20.3 Consensus size: 25
31316 TAATTTGTGA
*
31326 AATTACCGAATACCTTGTAGGGTAG
1 AATTACCGAATACCCTGTAGGGTAG
*
31351 AATTA-CGAA-ATCCTGT-GGGT-G
1 AATTACCGAATACCCTGTAGGGTAG
*
31372 -ATTACAGGAATACCCTGTAGGGTAG
1 AATTAC-CGAATACCCTGTAGGGTAG
* *
31397 AATTACCGGAATACACCTATATGGTAG
1 AATTACC-GAATAC-CCTGTAGGGTAG
*
31424 AATTACCGGATTACCCTGTAGGCGTAG
1 AATTACC-GAATACCCTGTAGG-GTAG
* *
31451 AATTA-GGAA-ATCCTGTAGGGTAG
1 AATTACCGAATACCCTGTAGGGTAG
31474 AATTATCCGCAAT-CCCTTGTAGGGTAG
1 AATTA-CCG-AATACCC-TGTAGGGTAG
31501 AATTACCGAAATACCCTGT-GGGTAG
1 AATTACCG-AATACCCTGTAGGGTAG
31526 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACC-GAATA-CCCTGTAGGGTAG
31553 AATTACCGAATA-CCTGTAGGGTAG
1 AATTACCGAATACCCTGTAGGGTAG
*
31577 AATTATCGCAATACCGCCTGTAGGGTAG
1 AATTACCG-AATA-C-CCTGTAGGGTAG
31605 AATTACCGAAATA-CCTGTAGGGTAG
1 AATTACCG-AATACCCTGTAGGGTAG
31630 AATTACCGGAATACCCTGTAGGGTTAG
1 AATTACC-GAATACCCTGTAGGG-TAG
* * *
31657 AATTA-C-TA-ACTCCTTTAAGGTAG
1 AATTACCGAATAC-CCTGTAGGGTAG
* *
31680 -A-TAGC-AACACCCTGTAGGGTAG
1 AATTACCGAATACCCTGTAGGGTAG
*
31702 AATTA-CGTATAACCCCTGTAGGGTAG
1 AATTACCGAAT-A-CCCTGTAGGGTAG
31728 AATTTACC-AAT--CCT-TA-GGTAG
1 AA-TTACCGAATACCCTGTAGGGTAG
*
31749 AAATACCGAAATACCCTGTA-GGTAG
1 AATTACCG-AATACCCTGTAGGGTAG
*
31774 AATTACTGAA-ATCCCTGTA-GGTAG
1 AATTACCGAATA-CCCTGTAGGGTAG
* * * *
31798 AATTACTGAGATACCTTGTGGGGTAA
1 AATTACCGA-ATACCCTGTAGGGTAG
31824 AATTACC
1 AATTACC
31831 ATTTTGCCCT
Statistics
Matches: 401, Mismatches: 35, Indels: 87
0.77 0.07 0.17
Matches are distributed among these distances:
20 8 0.02
21 10 0.02
22 25 0.06
23 33 0.08
24 73 0.18
25 73 0.18
26 79 0.20
27 76 0.19
28 24 0.06
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (25 bp):
AATTACCGAATACCCTGTAGGGTAG
Found at i:31514 original size:104 final size:103
Alignment explanation
Indices: 31326--31830 Score: 476
Period size: 104 Copynumber: 5.1 Consensus size: 103
31316 TAATTTGTGA
* * *
31326 AATTACC-GAATACCTTGTAGGGTAGAATTACGAAATCCTGT-GGGT-G-ATTA-CAGGAATACC
1 AATTACCGGAATACCCTGTAGGGTAGAATTACGAAATCCTGTAGGGTAGAATTATCCGCAATACC
* * *
31386 CTGTAGGGTAGAATTACCGGAATACACCTATATGGTAG
66 CTGTAGGGTAGAATTACCGAAATACACCTGTAGGGTAG
* *
31424 AATTACCGGATTACCCTGTAGGCGTAGAATTAGGAAATCCTGTAGGGTAGAATTATCCGCAAT-C
1 AATTACCGGAATACCCTGTAGG-GTAGAATTACGAAATCCTGTAGGGTAGAATTATCCGCAATAC
31488 CCTTGTAGGGTAGAATTACCGAAATAC-CCTGT-GGGTAG
65 CC-TGTAGGGTAGAATTACCGAAATACACCTGTAGGGTAG
31526 AATTACCGGAATACCCCTGTAGGGTAGAATTACCG-AATACCTGTAGGGTAGAATTAT-CGCAAT
1 AATTACCGGAATA-CCCTGTAGGGTAGAATTA-CGAAAT-CCTGTAGGGTAGAATTATCCGCAAT
31589 ACCGCCTGTAGGGTAGAATTACCGAAAT--ACCTGTAGGGTAG
63 A-C-CCTGTAGGGTAGAATTACCGAAATACACCTGTAGGGTAG
* * * * *
31630 AATTACCGGAATACCCTGTAGGGTTAGAATTACTAACTCCTTTAAGGTAG-A-TA---GCAACAC
1 AATTACCGGAATACCCTGTAGGG-TAGAATTACGAAATCCTGTAGGGTAGAATTATCCGCAATAC
* *
31690 CCTGTAGGGTAGAATTA-CG-TATAACCCCTGTAGGGTAG
65 CCTGTAGGGTAGAATTACCGAAAT-ACACCTGTAGGGTAG
* * *
31728 AATTTACC--AAT--CCT-TA-GGTAGAAATACCGAAATACCCTGTA-GGTAGAATTA-CTGAAA
1 AA-TTACCGGAATACCCTGTAGGGTAGAATTA-CGAAAT--CCTGTAGGGTAGAATTATCCGCAA
* * * * *
31785 T-CCCTGTA-GGTAGAATTACTGAGATAC-CTTGTGGGGTAA
62 TACCCTGTAGGGTAGAATTACCGAAATACACCTGTAGGGTAG
31824 AATTACC
1 AATTACC
31831 ATTTTGCCCT
Statistics
Matches: 349, Mismatches: 28, Indels: 63
0.79 0.06 0.14
Matches are distributed among these distances:
92 7 0.02
93 6 0.02
94 7 0.02
95 16 0.05
96 25 0.07
97 30 0.09
98 27 0.08
99 22 0.06
100 19 0.05
101 6 0.02
102 37 0.11
103 65 0.19
104 80 0.23
105 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (103 bp):
AATTACCGGAATACCCTGTAGGGTAGAATTACGAAATCCTGTAGGGTAGAATTATCCGCAATACC
CTGTAGGGTAGAATTACCGAAATACACCTGTAGGGTAG
Found at i:31530 original size:52 final size:51
Alignment explanation
Indices: 31326--31830 Score: 452
Period size: 51 Copynumber: 10.1 Consensus size: 51
31316 TAATTTGTGA
*
31326 AATTACCG-AATACCTTGTAGGGTAGAATTA-CGAAAT-CCTGT-GGGT-G
1 AATTACCGCAATACCCTGTAGGGTAGAATTACCGAAATACCTGTAGGGTAG
* * * * *
31372 -ATTACAGGAATACCCTGTAGGGTAGAATTACCGGAATACACCTATATGGTAG
1 AATTACCGCAATACCCTGTAGGGTAGAATTACC-GAA-ATACCTGTAGGGTAG
* * *
31424 AATTACCGGATTACCCTGTAGGCGTAGAATTA-GGAAAT-CCTGTAGGGTAG
1 AATTACCGCAATACCCTGTAGG-GTAGAATTACCGAAATACCTGTAGGGTAG
31474 AATTATCCGCAAT-CCCTTGTAGGGTAGAATTACCGAAATACCCTGT-GGGTAG
1 AATTA-CCGCAATACCC-TGTAGGGTAGAATTACCGAAATA-CCTGTAGGGTAG
*
31526 AATTACCGGAATACCCCTGTAGGGTAGAATTACCG-AATACCTGTAGGGTAG
1 AATTACCGCAATA-CCCTGTAGGGTAGAATTACCGAAATACCTGTAGGGTAG
*
31577 AATTATCGCAATACCGCCTGTAGGGTAGAATTACCGAAATACCTGTAGGGTAG
1 AATTACCGCAATA-C-CCTGTAGGGTAGAATTACCGAAATACCTGTAGGGTAG
* * * * *
31630 AATTACCGGAATACCCTGTAGGGTTAGAATTA-CTAACT-CCTTTAAGGTAG
1 AATTACCGCAATACCCTGTAGGG-TAGAATTACCGAAATACCTGTAGGGTAG
* **
31680 -A-TA--GCAACACCCTGTAGGGTAGAATTA-CGTATAACCCCTGTAGGGTAG
1 AATTACCGCAATACCCTGTAGGGTAGAATTACCG-A-AATACCTGTAGGGTAG
*
31728 AATTTA-C-CAAT--CCT-TA-GGTAGAAATACCGAAATACCCTGTA-GGTAG
1 AA-TTACCGCAATACCCTGTAGGGTAGAATTACCGAAATA-CCTGTAGGGTAG
* * * * * *
31774 AATTACTGAAAT-CCCTGTA-GGTAGAATTACTGAGATACCTTGTGGGGTAA
1 AATTACCGCAATACCCTGTAGGGTAGAATTACCGAAATACC-TGTAGGGTAG
31824 AATTACC
1 AATTACC
31831 ATTTTGCCCT
Statistics
Matches: 382, Mismatches: 42, Indels: 66
0.78 0.09 0.13
Matches are distributed among these distances:
45 18 0.05
46 45 0.12
47 21 0.05
48 24 0.06
49 26 0.07
50 56 0.15
51 67 0.18
52 62 0.16
53 54 0.14
54 9 0.02
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (51 bp):
AATTACCGCAATACCCTGTAGGGTAGAATTACCGAAATACCTGTAGGGTAG
Found at i:31534 original size:129 final size:127
Alignment explanation
Indices: 31341--31829 Score: 450
Period size: 129 Copynumber: 3.9 Consensus size: 127
31331 CCGAATACCT
*
31341 TGTAGGGTAGAATTA-CGAAATCCTGT-GGGT-G-ATTACAGGAATACCCTGTAGGGTAGAATTA
1 TGTAGGGTAGAATTACCGAAATCCTGTAGGGTAGAATTACCGGAATACCCTGTAGGGTAGAATTA
* * * *
31402 CCGGAATACACCTATATGGTAGAATTACCGGATTACCCTGTAGGCGTAGAATTA-GGAA-A-TCC
66 CCGGAATACACCTATAGGGTAGAATTACC-GAATA-CCTGTAGG-GTAGAATTACGCAATACGCC
* *
31464 TGTAGGGTAGAATTATCCGCAATCCCTTGTAGGGTAGAATTACCGAAATACCCTGT-GGGTAGAA
1 TGTAGGGTAGAATTA-CCGAAAT-CC-TGTAGGGTAGAATTACCGGAATACCCTGTAGGGTAGAA
* *
31528 TTACCGGAATACCCCTGTAGGGTAGAATTACCGAATACCTGTAGGGTAGAATTATCGCAATACCG
63 TTACCGGAATACACCTATAGGGTAGAATTACCGAATACCTGTAGGGTAGAATTA-CGCAATA-CG
31593 CC
126 CC
31595 TGTAGGGTAGAATTACCGAAATACCTGTAGGGTAGAATTACCGGAATACCCTGTAGGGTTAGAAT
1 TGTAGGGTAGAATTACCGAAAT-CCTGTAGGGTAGAATTACCGGAATACCCTGTAGGG-TAGAAT
* * * * * * * *
31660 TA-C--TA-ACTCCTTTAAGGTAG-A-TAGC-AACACCCTGTAGGGTAGAATTACG-TATAACCC
64 TACCGGAATACACCTATAGGGTAGAATTACCGAATA-CCTGTAGGGTAGAATTACGCAAT-ACGC
31717 C
127 C
* *
31718 TGTAGGGTAGAATTTACC--AATCCT-TA-GGTAGAAATACCGAAATACCCTGTA-GGTAGAATT
1 TGTAGGGTAGAA-TTACCGAAATCCTGTAGGGTAGAATTACCGGAATACCCTGTAGGGTAGAATT
* * * * * *
31778 ACTGAAAT-C-CCTGTA-GGTAGAATTACTGAGATACCTTGTGGGGTAAAATTAC
65 ACCGGAATACACCTATAGGGTAGAATTACCGA-ATACC-TGTAGGGTAGAATTAC
31830 CATTTTGCCC
Statistics
Matches: 310, Mismatches: 30, Indels: 53
0.79 0.08 0.13
Matches are distributed among these distances:
117 8 0.03
118 7 0.02
119 29 0.09
120 6 0.02
121 6 0.02
122 19 0.06
123 32 0.10
124 11 0.04
125 25 0.08
126 12 0.04
127 23 0.07
128 12 0.04
129 67 0.22
130 28 0.09
131 25 0.08
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (127 bp):
TGTAGGGTAGAATTACCGAAATCCTGTAGGGTAGAATTACCGGAATACCCTGTAGGGTAGAATTA
CCGGAATACACCTATAGGGTAGAATTACCGAATACCTGTAGGGTAGAATTACGCAATACGCC
Found at i:31701 original size:72 final size:70
Alignment explanation
Indices: 31600--31804 Score: 192
Period size: 72 Copynumber: 2.9 Consensus size: 70
31590 CCGCCTGTAG
*
31600 GGTAGAATTACCGAAATA-CCTGTAGGGTAGAATTACCGGAATACCCTGTAGGGTTAGAATTACT
1 GGTAGAA-TA-CGAAACACCCTGTAGGGTAGAATTACCGGAATACCCTGTAGGG-TAGAATTACT
31664 AACTCCTTTAA
63 AA-TCC-TT-A
* * *
31675 GGTAG-ATA-GCAACACCCTGTAGGGTAGAATTA-C-GTATAACCCCTGTAGGGTAGAATTTACC
1 GGTAGAATACGAAACACCCTGTAGGGTAGAATTACCGGAAT-A-CCCTGTAGGGTAGAA-TTACT
31736 AATCCTTA
63 AATCCTTA
* * *
31744 GGTAGAAATACCGAAATACCCTGTA-GGTAGAATTACTGAAAT-CCCTGTA-GGTAGAATTACT
1 GGTAG-AATA-CGAAACACCCTGTAGGGTAGAATTACCGGAATACCCTGTAGGGTAGAATTACT
31805 GAGATACCTT
Statistics
Matches: 110, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
69 10 0.09
70 12 0.11
71 24 0.22
72 43 0.39
73 13 0.12
74 3 0.03
75 5 0.05
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (70 bp):
GGTAGAATACGAAACACCCTGTAGGGTAGAATTACCGGAATACCCTGTAGGGTAGAATTACTAAT
CCTTA
Found at i:34266 original size:27 final size:26
Alignment explanation
Indices: 34202--34288 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
34192 TTAGTTTACC
* * *
34202 AAATTACTGAAATACCCCTCGACTTGTA
1 AAATTAC-CAAATACCCC-CGATTTATA
34230 AAATTACCAAAGT-CCCCCGATTTATA
1 AAATTACCAAA-TACCCCCGATTTATA
* *
34256 AAATTATCCAAATATCCTCGATTTAT-
1 AAATTA-CCAAATACCCCCGATTTATA
34282 AAATTAC
1 AAATTAC
34289 TGAAATAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.02
26 20 0.39
27 22 0.43
28 8 0.16
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.31
Consensus pattern (26 bp):
AAATTACCAAATACCCCCGATTTATA
Found at i:34333 original size:26 final size:26
Alignment explanation
Indices: 34304--34360 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
34294 TAAGATAGAT
* *
34304 ATTACCATTTTACCTCGATTTACAGA
1 ATTACCATTTTACCTCAATTTACAAA
34330 ATTACCATTTTACCTCAATTTACAAA
1 ATTACCATTTTACCTCAATTTACAAA
34356 ATTAC
1 ATTAC
34361 TGAAATACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (26 bp):
ATTACCATTTTACCTCAATTTACAAA
Found at i:34495 original size:26 final size:26
Alignment explanation
Indices: 34406--34676 Score: 249
Period size: 26 Copynumber: 10.7 Consensus size: 26
34396 CTCGATTAAT
* **
34406 AAATTCCCAAAATA-CCTTCTTTGTA
1 AAATTACCAAAATACCCTGGTTTGTA
*
34431 AAATTA-CTAAATACCCTTGGTTT-T-
1 AAATTACCAAAATACCC-TGGTTTGTA
*
34455 AAATCA-CAAAATACCCTGGTTTGTA
1 AAATTACCAAAATACCCTGGTTTGTA
* * *
34480 AAATTACCAAAATACCATGGCTTATA
1 AAATTACCAAAATACCCTGGTTTGTA
34506 AAATTACC-AAATACCCTGGTTTGTA
1 AAATTACCAAAATACCCTGGTTTGTA
*
34531 AAATTACCAAAATACCCATGGCTT-T-
1 AAATTACCAAAATACCC-TGGTTTGTA
*
34556 AAATCACC--AATACCCTGGTTTGT-
1 AAATTACCAAAATACCCTGGTTTGTA
* * **
34579 AAATTACAAAAAATATCCTTGGTTTACA
1 AAATTAC-CAAAATA-CCCTGGTTTGTA
* *
34607 AAACTACCAAAATACCCTAGTTTGTA
1 AAATTACCAAAATACCCTGGTTTGTA
** *
34633 AAATTACCAAAATACCCTAATTTGTG
1 AAATTACCAAAATACCCTGGTTTGTA
*
34659 AAATTACCGAAATACCCT
1 AAATTACCAAAATACCCT
34677 TGTAGGGTAG
Statistics
Matches: 202, Mismatches: 31, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
22 5 0.02
23 20 0.10
24 21 0.10
25 42 0.21
26 89 0.44
27 19 0.09
28 6 0.03
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (26 bp):
AAATTACCAAAATACCCTGGTTTGTA
Found at i:34725 original size:52 final size:51
Alignment explanation
Indices: 34660--35131 Score: 371
Period size: 52 Copynumber: 9.1 Consensus size: 51
34650 TAATTTGTGA
*
34660 AATTACCGAAATACCCTTGTAGGGTAGAATTACTAGAAATACCTGTAGGGTAG
1 AATTACCGGAATACCC-TGTAGGGTAGAATTAC-AGAAATACCTGTAGGGTAG
* * *
34713 AATT-CCGGAATACCCTGTAGGGTAG-ATTACCGGAATACACCTATAGGGTAG
1 AATTACCGGAATACCCTGTAGGGTAGAATTA-CAGAA-ATACCTGTAGGGTAG
* * *
34764 AATTACCGGATTACCCTGTAGGGTAGAATTACCGGAATACCCTTGTAGGGTAG
1 AATTACCGGAATACCCTGTAGGGTAGAATTACAGAAATA-CC-TGTAGGGTAG
* * *
34817 AATTATCGCAATACCCCTGTAGGGTAGAATTAC-GAAATCCCCTGTAGGGTAG
1 AATTACCGGAATA-CCCTGTAGGGTAGAATTACAGAAAT-ACCTGTAGGGTAG
*
34869 AATT-CCGGAATACCCTGTAGGGTAAGAATTACCGAAATACCCATGTAGGGTAG
1 AATTACCGGAATACCCTGTAGGGT-AGAATTACAGAAATA-CC-TGTAGGGTAG
* * *
34922 -ATT-TCGGAATACCCCTGTAGGGT-GAAATTACTA-AAATACCTTTTAAGGTAG
1 AATTACCGGAATA-CCCTGTAGGGTAG-AATTAC-AGAAATACC-TGTAGGGTAG
* * * ** **
34973 AATTA-TGCAACACCCCTGTAGGGTAGAATTA-ACGGTACCCCTGTAGGGTAG
1 AATTACCGGAATA-CCCTGTAGGGTAGAATTACA-GAAATACCTGTAGGGTAG
* * * *
35024 AATTTACCGAAATACCTTGT-GGGTAGAATAACCGAAATACCCTGTAGGGT-G
1 AA-TTACCGGAATACCCTGTAGGGTAGAATTACAGAAATA-CCTGTAGGGTAG
* * * * * *
35075 AATTACTGAAATA--CTGTAGGGTTAGAATTACTGAGAT-CCTTGTGGGGTAA
1 AATTACCGGAATACCCTGTAGGG-TAGAATTACAGAAATACC-TGTAGGGTAG
35125 AATTACC
1 AATTACC
35132 CATTTTGCCC
Statistics
Matches: 342, Mismatches: 49, Indels: 59
0.76 0.11 0.13
Matches are distributed among these distances:
48 5 0.01
49 10 0.03
50 47 0.14
51 80 0.23
52 122 0.36
53 59 0.17
54 19 0.06
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (51 bp):
AATTACCGGAATACCCTGTAGGGTAGAATTACAGAAATACCTGTAGGGTAG
Found at i:34735 original size:25 final size:26
Alignment explanation
Indices: 34660--35131 Score: 436
Period size: 25 Copynumber: 18.3 Consensus size: 26
34650 TAATTTGTGA
34660 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCC-TGTAGGGTAG
*
34687 AATTACTAGAAATA-CCTGTAGGGTAG
1 AATTAC-CGAAATACCCTGTAGGGTAG
*
34713 AATT-CCGGAATACCCTGTAGGGTAG
1 AATTACCGAAATACCCTGTAGGGTAG
* *
34738 -ATTACCGGAATACACCTATAGGGTAG
1 AATTACCGAAATAC-CCTGTAGGGTAG
* *
34764 AATTACCGGATTACCCTGTAGGGTAG
1 AATTACCGAAATACCCTGTAGGGTAG
*
34790 AATTACCGGAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCC-TGTAGGGTAG
* *
34817 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATA-CCCTGTAGGGTAG
*
34844 AATTA-CGAAATCCCCTGTAGGGTAG
1 AATTACCGAAATACCCTGTAGGGTAG
*
34869 AATT-CCGGAATACCCTGTAGGGTAAG
1 AATTACCGAAATACCCTGTAGGGT-AG
34895 AATTACCGAAATACCCATGTAGGGTAG
1 AATTACCGAAATACCC-TGTAGGGTAG
* *
34922 -ATT-TCGGAATACCCCTGTAGGGT-G
1 AATTACCGAAATA-CCCTGTAGGGTAG
** * * *
34946 AAATTACTAAAATACCTTTTAAGGTAG
1 -AATTACCGAAATACCCTGTAGGGTAG
* * *
34973 AATTA-TGCAACACCCCTGTAGGGTAG
1 AATTACCGAAATA-CCCTGTAGGGTAG
* *
34999 AATTAACG--GTACCCCTGTAGGGTAG
1 AATTACCGAAATA-CCCTGTAGGGTAG
*
35024 AATTTACCGAAATACCTTGT-GGGTAG
1 AA-TTACCGAAATACCCTGTAGGGTAG
*
35050 AATAACCGAAATACCCTGTAGGGT-G
1 AATTACCGAAATACCCTGTAGGGTAG
*
35075 AATTACTGAAATA--CTGTAGGGTTAG
1 AATTACCGAAATACCCTGTAGGG-TAG
* * * * *
35100 AATTACTGAGAT-CCTTGTGGGGTAA
1 AATTACCGAAATACCCTGTAGGGTAG
35125 AATTACC
1 AATTACC
35132 CATTTTGCCC
Statistics
Matches: 375, Mismatches: 44, Indels: 54
0.79 0.09 0.11
Matches are distributed among these distances:
23 8 0.02
24 10 0.03
25 137 0.37
26 122 0.33
27 79 0.21
28 19 0.05
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (26 bp):
AATTACCGAAATACCCTGTAGGGTAG
Found at i:34890 original size:130 final size:129
Alignment explanation
Indices: 34660--35131 Score: 479
Period size: 130 Copynumber: 3.7 Consensus size: 129
34650 TAATTTGTGA
* * *
34660 AATTACCGAAATACCCTTGTAGGGTAGAATTACTAGAAATA-CCTGTAGGGTAGAATTCCGGAAT
1 AATTACCGAAATACCCTTGTAGGGT-GAATTA-TCGAAATACCCTGTAGGGTAGAATTACGAAAT
* * * *
34724 ACCCTGTAGGGTAG-ATTACCGGAATACACCTATAGGGTAGAATTACCGGATTACCCTGTAGGGT
64 CCCCTGTAGGGTAGAATTACCGGAATAC-CCTGTAGGGTAGAATTACCGAAATACCCTGTAGGGT
34788 AG
128 AG
* *
34790 AATTACCGGAATACCCTTGTAGGGTAGAATTATCGCAATACCCCTGTAGGGTAGAATTACGAAAT
1 AATTACCGAAATACCCTTGTAGGGT-GAATTATCGAAATA-CCCTGTAGGGTAGAATTACGAAAT
34855 CCCCTGTAGGGTAGAATT-CCGGAATACCCTGTAGGGTAAGAATTACCGAAATACCCATGTAGGG
64 CCCCTGTAGGGTAGAATTACCGGAATACCCTGTAGGGT-AGAATTACCGAAATACCC-TGTAGGG
34919 TAG
127 TAG
* * * * * * * *
34922 -ATT-TCGGAATACCCCTGTAGGGTGAAATTA-CTAAAATACCTTTTAAGGTAGAATTATGCAAC
1 AATTACCGAAATACCCTTGTAGGGTG-AATTATC-GAAATACCCTGTAGGGTAGAATTACG-AA-
* *
34984 A-CCCCTGTAGGGTAGAATTAACGG--TACCCCTGTAGGGTAGAATTTACCGAAATACCTTGT-G
62 ATCCCCTGTAGGGTAGAATTACCGGAATA-CCCTGTAGGGTAGAA-TTACCGAAATACCCTGTAG
35045 GGTAG
125 GGTAG
* *
35050 AATAACCGAAATACCC-TGTAGGGTGAATTA-CTGAAATA--CTGTAGGGTTAGAATTACTGAGA
1 AATTACCGAAATACCCTTGTAGGGTGAATTATC-GAAATACCCTGTAGGG-TAGAATTAC-GAAA
* * *
35111 T-CCTTGTGGGGTAAAATTACC
63 TCCCCTGTAGGGTAGAATTACC
35132 CATTTTGCCC
Statistics
Matches: 293, Mismatches: 32, Indels: 38
0.81 0.09 0.10
Matches are distributed among these distances:
126 22 0.08
127 9 0.03
128 19 0.06
129 44 0.15
130 120 0.41
131 66 0.23
132 13 0.04
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (129 bp):
AATTACCGAAATACCCTTGTAGGGTGAATTATCGAAATACCCTGTAGGGTAGAATTACGAAATCC
CCTGTAGGGTAGAATTACCGGAATACCCTGTAGGGTAGAATTACCGAAATACCCTGTAGGGTAG
Found at i:35582 original size:37 final size:37
Alignment explanation
Indices: 35524--35644 Score: 179
Period size: 37 Copynumber: 3.3 Consensus size: 37
35514 GGATTTGCAT
* *
35524 TTCTGATTCTGTCACCTAATTCTAATTCTGATTCTGA
1 TTCTGATTCTGTCACCAAATTCTGATTCTGATTCTGA
* * * *
35561 TTTTGATTTTGTCAACAAATTCTGATTCTGATTTTGA
1 TTCTGATTCTGTCACCAAATTCTGATTCTGATTCTGA
*
35598 TTCTGATTCTGTCACCGAATTCTGATTCTGATTCTGA
1 TTCTGATTCTGTCACCAAATTCTGATTCTGATTCTGA
35635 TTCTGATTCT
1 TTCTGATTCT
35645 AGTTGTGATA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (37 bp):
TTCTGATTCTGTCACCAAATTCTGATTCTGATTCTGA
Found at i:35588 original size:6 final size:6
Alignment explanation
Indices: 35579--35644 Score: 80
Period size: 6 Copynumber: 10.8 Consensus size: 6
35569 TTGTCAACAA
* * *
35579 ATTCTG ATTCTG ATTTTG ATTCTG ATTCTG -TCACCG AATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT-TCTG -ATTCTG ATTCTG
35628 ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCT
35645 AGTTGTGATA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
5 1 0.02
6 47 0.92
7 2 0.04
8 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:37878 original size:25 final size:25
Alignment explanation
Indices: 37845--37934 Score: 71
Period size: 25 Copynumber: 3.6 Consensus size: 25
37835 CCCGGTTTGT
*
37845 AATTTCAAAAATACCTTGTTGATAA
1 AATTACAAAAATACCTTGTTGATAA
*
37870 AATTAC-AAAATACGCCTGATTTG-TAA
1 AATTACAAAAATAC-CTTG--TTGATAA
* *
37896 AATTACCAAAATACCCTTGTTTA-AA
1 AATTACAAAAATA-CCTTGTTGATAA
*
37921 AATTA-AGAAATACC
1 AATTACAAAAATACC
37935 CTAGTTTGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
23 2 0.04
24 12 0.23
25 17 0.32
26 9 0.17
27 12 0.23
28 1 0.02
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.31
Consensus pattern (25 bp):
AATTACAAAAATACCTTGTTGATAA
Found at i:37899 original size:26 final size:25
Alignment explanation
Indices: 37867--37963 Score: 89
Period size: 24 Copynumber: 3.9 Consensus size: 25
37857 ACCTTGTTGA
37867 TAAAATTACAAAATACGCCTGATTTG
1 TAAAATTACAAAATAC-CCTGATTTG
37893 TAAAATTACCAAAATACCCTTG-TTT-
1 TAAAATTA-CAAAATACCC-TGATTTG
*
37918 AAAAATTA-AGAAATACCCT-AGTTTG
1 TAAAATTACA-AAATACCCTGA-TTTG
37943 T--AATTACTAAAATACCCTGAT
1 TAAAATTAC-AAAATACCCTGAT
37964 GTGAAATTCC
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
23 7 0.12
24 21 0.35
25 9 0.15
26 13 0.22
27 10 0.17
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.32
Consensus pattern (25 bp):
TAAAATTACAAAATACCCTGATTTG
Found at i:37909 original size:51 final size:47
Alignment explanation
Indices: 37831--37958 Score: 127
Period size: 51 Copynumber: 2.6 Consensus size: 47
37821 TTAAAATCAC
* * *
37831 AATACCC-GGTTTGTAATTTCAAAAATACCTTGTTGATAAAATTACA-A
1 AATACCCTAGTTTGTAATTACCAAAATACCTTGTTGA-AAAATTA-AGA
*
37878 AATACGCCT-GATTTGTAAAATTACCAAAATACCCTTGTTTAAAAATTAAGA
1 AATAC-CCTAG-TTTGT--AATTACCAAAATA-CCTTGTTGAAAAATTAAGA
*
37929 AATACCCTAGTTTGTAATTACTAAAATACC
1 AATACCCTAGTTTGTAATTACCAAAATACC
37959 CTGATGTGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
47 7 0.10
48 15 0.22
49 5 0.07
50 9 0.13
51 25 0.36
52 8 0.12
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.33
Consensus pattern (47 bp):
AATACCCTAGTTTGTAATTACCAAAATACCTTGTTGAAAAATTAAGA
Found at i:38009 original size:50 final size:49
Alignment explanation
Indices: 37944--38160 Score: 128
Period size: 50 Copynumber: 4.3 Consensus size: 49
37934 CCTAGTTTGT
* *
37944 AATTACTAAAATACCCTGATGT-GAAATTC-CGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCTGATGTAG-AA-TCACG-AATACCCCTGTAGGGTAG
* *
37994 AATTACTGAAATACCCTTGGTGTAGAATCACGGATACCCCTGTAGGGTAG
1 AATTACTGAAATACCC-TGATGTAGAATCACGAATACCCCTGTAGGGTAG
* * *
38044 AATT-CCGAGAATACCCTGTAGGGTTAGAATTATCGCAAGTA-CCCTGTA-GGTAG
1 AATTACTGA-AATACCCTG-A-TG-TAGAATCA-CG-AA-TACCCCTGTAGGGTAG
* * * **
38097 AATTAC-GGAAT-CCCTGTAGGGTAGAATTACCGGAATAAACCTGTAGGGTAG
1 AATTACTGAAATACCCTG-A-TGTAGAATCA-C-GAATACCCCTGTAGGGTAG
38148 AATTA-TG-AATACC
1 AATTACTGAAATACC
38161 TGTAGGGTGA
Statistics
Matches: 139, Mismatches: 12, Indels: 31
0.76 0.07 0.17
Matches are distributed among these distances:
49 7 0.05
50 64 0.46
51 34 0.24
52 11 0.08
53 12 0.09
54 9 0.06
55 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (49 bp):
AATTACTGAAATACCCTGATGTAGAATCACGAATACCCCTGTAGGGTAG
Found at i:38075 original size:77 final size:74
Alignment explanation
Indices: 37968--38166 Score: 237
Period size: 77 Copynumber: 2.6 Consensus size: 74
37958 CCTGATGTGA
*
37968 AATTCCGA-AATACCCTTGTAGGGTAGAATTACTGAAATACCCT-TGGTGTAGAATCACGGATAC
1 AATTCCGAGAATACCC-TGTAGGGTAGAATTA-TGAAATACCCTGTAG-GTAGAATCACGGA-AC
38031 CCCTGTAGGGTAG
62 CCCTGTAGGGTAG
* * *
38044 AATTCCGAGAATACCCTGTAGGGTTAGAATTATCGCAAGTACCCTGTAGGTAGAATTACGGAATC
1 AATTCCGAGAATACCCTGTAGGG-TAGAATTAT-G-AAATACCCTGTAGGTAGAATCACGGAACC
38109 CCTGTAGGGTAG
63 CCTGTAGGGTAG
*
38121 AATTACCG-GAATAAACCTGTAGGGTAGAATTATG-AATA-CCTGTAGG
1 AATT-CCGAGAAT-ACCCTGTAGGGTAGAATTATGAAATACCCTGTAGG
38167 GTGATTACGG
Statistics
Matches: 110, Mismatches: 6, Indels: 17
0.83 0.05 0.13
Matches are distributed among these distances:
73 8 0.07
74 3 0.03
76 17 0.15
77 47 0.43
78 33 0.30
79 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (74 bp):
AATTCCGAGAATACCCTGTAGGGTAGAATTATGAAATACCCTGTAGGTAGAATCACGGAACCCCT
GTAGGGTAG
Found at i:38115 original size:23 final size:25
Alignment explanation
Indices: 37976--38383 Score: 294
Period size: 25 Copynumber: 16.8 Consensus size: 25
37966 GAAATTCCGA
*
37976 AATACCCTTGTAGGGTAGAATTACTGA
1 AATACCC-TGTAGGGTAGAATTAC-GG
*
38003 AATACCCT-T-GGTGTAGAATCACGG
1 AATACCCTGTAGG-GTAGAATTACGG
*
38027 -ATACCCCTGTAGGGTAGAATTCCGAG
1 AATA-CCCTGTAGGGTAGAATTACG-G
*
38053 AATACCCTGTAGGGTTAGAATTATCGC
1 AATACCCTGTAGGG-TAGAATTA-CGG
38080 AAGTACCCTGTA-GGTAGAATTACGG
1 AA-TACCCTGTAGGGTAGAATTACGG
38105 AAT-CCCTGTAGGGTAGAATTACCGG
1 AATACCCTGTAGGGTAGAATTA-CGG
* *
38130 AATAAACCTGTAGGGTAGAATTA-TG
1 AAT-ACCCTGTAGGGTAGAATTACGG
38155 AATA-CCTGTAGGGT-G-ATTACGG
1 AATACCCTGTAGGGTAGAATTACGG
* * *
38177 AAT-CCC-CTATGGTAGAATTATCGC
1 AATACCCTGTAGGGTAGAATTA-CGG
** * *
38201 AATACCCCATAGGGTAG-GTTACCG
1 AATACCCTGTAGGGTAGAATTACGG
* *
38225 --TACCCTGTA-GGT-GAAATTCCAG
1 AATACCCTGTAGGGTAG-AATTACGG
** *
38247 AAT-CCCT-TATCGTAGAATT-CTG
1 AATACCCTGTAGGGTAGAATTACGG
* *
38269 AATACCCTGTAGGGTAGAATTTCTG
1 AATACCCTGTAGGGTAGAATTACGG
*
38294 AATACCCTGTAAGGGTAG-ATTTC-G
1 AATACCCTGT-AGGGTAGAATTACGG
*
38318 -ATAGCCTGTAGGGTAGAATTACGG
1 AATACCCTGTAGGGTAGAATTACGG
*
38342 -ATA-CCTGT-GGGTAGAATTACTG
1 AATACCCTGTAGGGTAGAATTACGG
38364 AA-ATCCCTGTAGGGT-GAATT
1 AATA-CCCTGTAGGGTAGAATT
38384 GCCGAAAATA
Statistics
Matches: 315, Mismatches: 30, Indels: 75
0.75 0.07 0.18
Matches are distributed among these distances:
20 1 0.00
21 12 0.04
22 47 0.15
23 56 0.18
24 52 0.17
25 62 0.20
26 36 0.11
27 38 0.12
28 11 0.03
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (25 bp):
AATACCCTGTAGGGTAGAATTACGG
Found at i:38331 original size:22 final size:23
Alignment explanation
Indices: 38274--38359 Score: 97
Period size: 22 Copynumber: 3.7 Consensus size: 23
38264 TTCTGAATAC
*
38274 CCTGTAGGGTAGAATTTCTGAATA
1 CCTGTAGGGTAGAATTTC-GGATA
38298 CCCTGTAAGGGTAG-ATTTC-GATA
1 -CCTGT-AGGGTAGAATTTCGGATA
*
38321 GCCTGTAGGGTAGAATTACGGATA
1 -CCTGTAGGGTAGAATTTCGGATA
38345 CCTGT-GGGTAGAATT
1 CCTGTAGGGTAGAATT
38360 ACTGAAATCC
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
22 17 0.31
23 17 0.31
24 4 0.07
25 10 0.18
26 7 0.13
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (23 bp):
CCTGTAGGGTAGAATTTCGGATA
Found at i:38333 original size:142 final size:141
Alignment explanation
Indices: 38082--38338 Score: 308
Period size: 142 Copynumber: 1.8 Consensus size: 141
38072 ATTATCGCAA
* *
38082 GTACCCTGTAGGTAGAATTACGGAATCCCTGTAGGGTAGAATTACCGGAATAAACCTGTAGGGTA
1 GTACCCTGTAGGTAGAATTACAGAATCCCTGTAGCGTAGAATTA-CGGAATAAACCTGTAGGGTA
* *
38147 GAATTATGAATACCTGTAGGGTGATTACGGAATCCCCTATGGTAGAATTATCGCAATACCCCATA
65 GAATTATGAATACCTGTAGGGTGATTACGGAAGCCCCTAGGGTAGAATTATCGCAATACCCCATA
38212 GGGTAGGTTACC
130 GGGTAGGTTACC
* * * *
38224 GTACCCTGTAGGT-GAAATTCCAGAATCCCT-TATCGTAGAATT-CTGAAT-ACCCTGTAGGGTA
1 GTACCCTGTAGGTAG-AATTACAGAATCCCTGTAGCGTAGAATTACGGAATAAACCTGTAGGGTA
* * **
38285 GAATTTCTGAATACCCTGTAAGGGTAGATTTC-GATAGCCTGTAGGGTAGAATTA
65 GAA-TTATGAATA-CCTGT-AGGGT-GATTACGGA-AGCCCCTAGGGTAGAATTA
38339 CGGATACCTG
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
138 15 0.15
139 13 0.13
140 5 0.05
141 18 0.19
142 46 0.47
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (141 bp):
GTACCCTGTAGGTAGAATTACAGAATCCCTGTAGCGTAGAATTACGGAATAAACCTGTAGGGTAG
AATTATGAATACCTGTAGGGTGATTACGGAAGCCCCTAGGGTAGAATTATCGCAATACCCCATAG
GGTAGGTTACC
Found at i:38360 original size:22 final size:24
Alignment explanation
Indices: 37977--38383 Score: 226
Period size: 23 Copynumber: 16.8 Consensus size: 24
37967 AAATTCCGAA
*
37977 ATACCCTTGTAGGGTAGAATTACTGAA
1 ATACCC-TGTAGGGTAGAATTAC-G-G
*
38004 ATACCCT-T-GGTGTAGAATCACGG
1 ATACCCTGTAGG-GTAGAATTACGG
*
38027 ATACCCCTGTAGGGTAGAATTCCGAG
1 ATA-CCCTGTAGGGTAGAATTACG-G
*
38053 AATACCCTGTAGGGTTAGAATTATCGCA
1 -ATACCCTGTAGGG-TAGAATTA-CG-G
38081 AGTACCCTGTA-GGTAGAATTACGG
1 A-TACCCTGTAGGGTAGAATTACGG
38105 A-ATCCCTGTAGGGTAGAATTACCGG
1 ATA-CCCTGTAGGGTAGAATTA-CGG
* * *
38130 AATAAACCTGTAGGGTAGAATTATGA
1 -AT-ACCCTGTAGGGTAGAATTACGG
38156 ATA-CCTGTAGGGT-G-ATTACGG
1 ATACCCTGTAGGGTAGAATTACGG
* * *
38177 A-ATCCC-CTATGGTAGAATTATCGCA
1 ATA-CCCTGTAGGGTAGAATTA-CG-G
** * *
38202 ATACCCCATAGGGTAG-GTTACCG
1 ATACCCTGTAGGGTAGAATTACGG
* *
38225 -TACCCTGTA-GGT-GAAATTCCAG
1 ATACCCTGTAGGGTAG-AATTACGG
** *
38247 A-ATCCCT-TATCGTAGAATT-CTGA
1 ATA-CCCTGTAGGGTAGAATTAC-GG
* *
38270 ATACCCTGTAGGGTAGAATTTCTGA
1 ATACCCTGTAGGGTAGAATTAC-GG
*
38295 ATACCCTGTAAGGGTAG-ATTTC-G
1 ATACCCTGT-AGGGTAGAATTACGG
*
38318 ATAGCCTGTAGGGTAGAATTACGG
1 ATACCCTGTAGGGTAGAATTACGG
*
38342 ATA-CCTGT-GGGTAGAATTACTG
1 ATACCCTGTAGGGTAGAATTACGG
*
38364 AAATCCCTGTAGGGT-GAATT
1 ATA-CCCTGTAGGGTAGAATT
38384 GCCGAAAATA
Statistics
Matches: 305, Mismatches: 36, Indels: 81
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.01
21 14 0.05
22 42 0.14
23 56 0.18
24 48 0.16
25 56 0.18
26 39 0.13
27 36 0.12
28 12 0.04
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (24 bp):
ATACCCTGTAGGGTAGAATTACGG
Found at i:38390 original size:24 final size:26
Alignment explanation
Indices: 38322--38428 Score: 70
Period size: 25 Copynumber: 4.3 Consensus size: 26
38312 ATTTCGATAG
*
38322 CCTGTAGGGTAGAATTA-CG--GATA-
1 CCTGTAGGGT-GAATTACCGAAAATAC
*
38345 CCTGT-GGGTAGAATTACTG-AAAT-C
1 CCTGTAGGGT-GAATTACCGAAAATAC
*
38369 CCTGTAGGGTGAATTGCCGAAAATAC
1 CCTGTAGGGTGAATTACCGAAAATAC
* *
38395 CTTGTAAGGGTGAAATACC--AAATAC
1 CCTGT-AGGGTGAATTACCGAAAATAC
*
38420 CTTGTAGGG
1 CCTGTAGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
22 11 0.16
23 6 0.09
24 18 0.26
25 19 0.27
26 5 0.07
27 11 0.16
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (26 bp):
CCTGTAGGGTGAATTACCGAAAATAC
Done.