Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1200
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: 192638
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:146896 original size:150 final size:148
Alignment explanation
Indices: 146735--147147 Score: 531
Period size: 150 Copynumber: 2.8 Consensus size: 148
146725 TGTGTTGAGA
* * * * *
146735 CAAGGCCAGCGACATTGGGCTCAGGAATATTAAAGACGCCAATATGCTGATTCAGGGCCAACGAT
1 CAAGGCCAGCGACATTGGACTTA--AAAATGAAAGACGCCAATATGCTGATTCAAGGCCAACGAT
* *** *
146800 ATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGGCATTGGTCTTAAAGATG
64 ATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACACCAGACTTAAAGATG
* *
146865 ACGGTGCCAATATGCTGATT
129 AAGATGCCAATATGCTGATT
* * * * * * * *
146885 CAAGGCTAGCGATATCGGACTTAAAAATGAAA-ATGCCAATGTACTGATTCAAGGCCAGCGACAT
1 CAAGGCCAGCGACATTGGACTTAAAAATGAAAGACGCCAATATGCTGATTCAAGGCCAACGATAT
* * *
146949 TGGACTTAAAGATGACGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATACCAGACTTAAAGAT
66 TGGACTTAAAGAT---GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACACCAGACTTAAAGAT
147014 GAAGATGCCAATATGCTGATT
128 GAAGATGCCAATATGCTGATT
* *
147035 CAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGCGCCAATATGCTGATTCAAGGCCAACGAT
1 CAAGGCCAGCGACATTGGACTTAAAAATGA--AAGACGCCAATATGCTGATTCAAGGCCAACGAT
147100 ATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
64 ATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
147148 TAAGAAAAGT
Statistics
Matches: 222, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
147 39 0.18
148 7 0.03
150 135 0.61
152 2 0.01
153 39 0.18
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (148 bp):
CAAGGCCAGCGACATTGGACTTAAAAATGAAAGACGCCAATATGCTGATTCAAGGCCAACGATAT
TGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACACCAGACTTAAAGATGAA
GATGCCAATATGCTGATT
Found at i:148363 original size:79 final size:78
Alignment explanation
Indices: 148239--148449 Score: 246
Period size: 79 Copynumber: 2.7 Consensus size: 78
148229 TGAGAAATTT
* * *
148239 AATATTTTGGAGATAATAA-CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCC
1 AATATTTAGGAAATAA-AACCGGGGTTGGAGTATCCCCTCG-AAATAACGGGGTTGGAGTATCCC
** *
148303 CGGTTGTGAAAAATC
64 CAATTATGAAAAATC
* * *
148318 GATGA-TTAGGAAATAAAATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCC
1 AAT-ATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCC
*
148382 CAATTATGAGAAATC
64 CAATTATGAAAAATC
* * *
148397 AATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGAAGGTAACGGGGT
1 AATATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTCGAA-ATAACGGGGT
148450 AACGAGGTTA
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
78 6 0.05
79 104 0.93
80 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.26
Consensus pattern (78 bp):
AATATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAATAACGGGGTTGGAGTATCCCCA
ATTATGAAAAATC
Found at i:148587 original size:51 final size:51
Alignment explanation
Indices: 148455--148587 Score: 128
Period size: 51 Copynumber: 2.6 Consensus size: 51
148445 GGGGTAACGA
* * *
148455 GGTTAGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAACAAAATCGG
1 GGTTGGAGTATCCCCGATTATG-AAAATTGGTGTTTTTGGAAACAAAATCGG
* * * * *
148507 AGTTGGAGTAT-CCCAATTAAAGGAAAATTGGTG-TTTT-GAGCATAAAATCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAATTGGTGTTTTTGGA-AACAAAATCGG
148558 GGTTGGAGTATCCCCGATTATGAACAATTG
1 GGTTGGAGTATCCCCGATTATGAA-AATTG
148588 AGAAACTTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
50 6 0.09
51 33 0.51
52 25 0.38
53 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAATTGGTGTTTTTGGAAACAAAATCGG
Found at i:150967 original size:13 final size:13
Alignment explanation
Indices: 150949--150974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
150939 ACAAAGATCG
150949 ATGTATCGATACA
1 ATGTATCGATACA
150962 ATGTATCGATACA
1 ATGTATCGATACA
150975 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:150985 original size:21 final size:21
Alignment explanation
Indices: 150961--151002 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
150951 GTATCGATAC
150961 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
150982 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
151003 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:151184 original size:49 final size:49
Alignment explanation
Indices: 151109--151872 Score: 676
Period size: 49 Copynumber: 15.9 Consensus size: 49
151099 GCACCTTAAC
* * * * * *
151109 CATCTTTAAGTCTAATGTTGCCGGCCTTGAATTAGCACATTGACGTCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * *
151158 TATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * *
151207 CATCTTTAAGACCAATGTTGCTGGCCTTGAATCAACACATTGG------
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * * *
151250 CA-C---AAG-CACAATATCGCTGGCCTTGATTCAGCATATTGGCACCTT
1 CATCTTTAAGTC-CAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * * * * * *
151295 CATCTTTAAGACCGATGTCGTTGGCCTTGAATTAGAATATTGGCACCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * * *
151344 AACCATCTTTAAGTCCAATGTCGCCGACCTTGAATCAGCACATTAGCGTCTT
1 ---CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* *
151396 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* *
151445 CATCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTGG------
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * * * * *
151488 CA----TAAGCCCAATATCACTGGCCTTGACTCAGCATATTGGCACCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * * *
151533 CATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATTGGCACCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* *
151582 AACCATCTTTAAGTCTAATGTCGCCGGCCTTGAATCAGCACATTGGCATCTT
1 ---CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * * *
151634 CATCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTAGCATCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * * *
151683 CATCATTAAGACCAATGTCGCTGGCCTTGAATCAGCACAATGGCACCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * *** *
151732 CATCTTTAAGTCCGATATTATTGGCCTTGAATCAGCATATTGGCATCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
* * **
151781 TAACATTCCTAAGTCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCATTCTT
1 CATC-TT--TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-TCTT
* ** *
151834 --T-TTTAAATTTAATGTCGCTGGCCATGAATCAGCACATTG
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
151873 TCATTTTTCG
Statistics
Matches: 576, Mismatches: 107, Indels: 66
0.77 0.14 0.09
Matches are distributed among these distances:
38 1 0.00
39 60 0.10
42 1 0.00
43 4 0.01
45 4 0.01
46 1 0.00
47 30 0.05
49 356 0.62
50 3 0.01
52 112 0.19
53 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT
Found at i:151510 original size:39 final size:39
Alignment explanation
Indices: 151451--151528 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
151441 TCTTCATCTT
* *
151451 TAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCA
1 TAAGACCAATATCACTGGCCTTGAATCAACACATTGGCA
* * * *
151490 TAAGCCCAATATCACTGGCCTTGACTCAGCATATTGGCA
1 TAAGACCAATATCACTGGCCTTGAATCAACACATTGGCA
151529 CCTTCATCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (39 bp):
TAAGACCAATATCACTGGCCTTGAATCAACACATTGGCA
Found at i:151511 original size:189 final size:187
Alignment explanation
Indices: 151316--151665 Score: 495
Period size: 189 Copynumber: 1.9 Consensus size: 187
151306 CCGATGTCGT
* *
151316 TGGCCTTGAATTAGAATATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCGACCTTGAATCA
1 TGGCCTTGAATCAGAATATTGGCACCTT---CATCTTTAAGACCAATGTCGCCGACCTTGAATCA
** * *
151381 GCACATTAGCGTCTT-CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
63 GCACATTAGCACCTTACATCTTTAAGTCCAATATCGCCGGCCTTGAATCAGCACATTGGCATCTT
*
151445 CATCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCATAAGCCCAATATCAC
128 CATCTTTAAGACCAATATCGCTGGCCTTGAATCAACACATTGGCATAAGCCCAATATCAC
* * * ** *
151505 TGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGAATATTGGCACCTTCATCTTTAAGACCAATGTCGCCGACCTTGAATCAGCA
* * *
151570 CATTGGCACCTTAACCATCTTTAAGTCTAATGTCGCCGGCCTTGAATCAGCACATTGGCATCTTC
66 CATTAGCACCTT-A-CATCTTTAAGTCCAATATCGCCGGCCTTGAATCAGCACATTGGCATCTTC
*
151635 ATCTTTAAGTCCAATATCGCTGGCCTTGAAT
129 ATCTTTAAGACCAATATCGCTGGCCTTGAAT
151666 TAGCATATTA
Statistics
Matches: 141, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
186 41 0.29
189 100 0.71
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (187 bp):
TGGCCTTGAATCAGAATATTGGCACCTTCATCTTTAAGACCAATGTCGCCGACCTTGAATCAGCA
CATTAGCACCTTACATCTTTAAGTCCAATATCGCCGGCCTTGAATCAGCACATTGGCATCTTCAT
CTTTAAGACCAATATCGCTGGCCTTGAATCAACACATTGGCATAAGCCCAATATCAC
Found at i:151521 original size:238 final size:237
Alignment explanation
Indices: 151098--151728 Score: 1064
Period size: 238 Copynumber: 2.6 Consensus size: 237
151088 GGTGTCTACA
* * *
151098 GGCACCTTAACCATCTTTAAGTCTAATGTTGCCGGCCTTGAATTAGCACATTGACGTCTTTATCT
1 GGCACCTTAACCATCTTTAAGTCTAATGTCGCCGGCCTTGAATCAGCACATTG-CGTCTTCATCT
*
151163 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTTGC
65 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTCGC
* *
151228 TGGCCTTGAATCAACACATTGGCACAAGCACAATATCGCTGGCCTTGATTCAGCATATTGGCACC
130 TGGCCTTGAATCAACACATTGGCACAAGCACAATATCACTGGCCTTGACTCAGCATATTGGCACC
* *
151293 TTCATCTTTAAGACCGATGTCGTTGGCCTTGAATTAGAATATT
195 TTCATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGAACATT
* *
151336 GGCACCTTAACCATCTTTAAGTCCAATGTCGCCGACCTTGAATCAGCACATTAGCGTCTTCATCT
1 GGCACCTTAACCATCTTTAAGTCTAATGTCGCCGGCCTTGAATCAGCACATT-GCGTCTTCATCT
151401 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTCGC
65 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTCGC
* *
151466 TGGCCTTGAATCAACACATTGGCATAAGCCCAATATCACTGGCCTTGACTCAGCATATTGGCACC
130 TGGCCTTGAATCAACACATTGGCACAAGCACAATATCACTGGCCTTGACTCAGCATATTGGCACC
*
151531 TTCATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATT
195 TTCATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGAACATT
*
151574 GGCACCTTAACCATCTTTAAGTCTAATGTCGCCGGCCTTGAATCAGCACATTGGCATCTTCATCT
1 GGCACCTTAACCATCTTTAAGTCTAATGTCGCCGGCCTTGAATCAGCACATT-GCGTCTTCATCT
* * *
151639 TTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTAGCATCTTCATCATTAAGACCAATGTCGC
65 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTCGC
* *
151704 TGGCCTTGAATCAGCACAATGGCAC
130 TGGCCTTGAATCAACACATTGGCAC
151729 CTTCATCTTT
Statistics
Matches: 369, Mismatches: 23, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
238 368 1.00
239 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (237 bp):
GGCACCTTAACCATCTTTAAGTCTAATGTCGCCGGCCTTGAATCAGCACATTGCGTCTTCATCTT
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTCGCT
GGCCTTGAATCAACACATTGGCACAAGCACAATATCACTGGCCTTGACTCAGCATATTGGCACCT
TCATCTTTAAGACCGATGTCGTTGGCCTTGAATCAGAACATT
Found at i:151558 original size:88 final size:88
Alignment explanation
Indices: 151402--151577 Score: 289
Period size: 88 Copynumber: 2.0 Consensus size: 88
151392 TCTTCATCTT
* * *
151402 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTCGCT
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCT
151467 GGCCTTGAATCAACACATTGGCA
66 GGCCTTGAATCAACACATTGGCA
* * *
151490 TAAGCCCAATATCACTGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTT
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCT
*
151555 GGCCTTGAATCAGCACATTGGCA
66 GGCCTTGAATCAACACATTGGCA
151578 CCTTAACCAT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (88 bp):
TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCT
GGCCTTGAATCAACACATTGGCA
Found at i:151794 original size:150 final size:148
Alignment explanation
Indices: 151490--151812 Score: 405
Period size: 150 Copynumber: 2.2 Consensus size: 148
151480 CACATTGGCA
* * * * * * *
151490 TAAGCCCAATATCACTGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTCATCATTAAGACCAATGTCGCT
* * * *
151555 GGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCTAATGTCGCCGGCCTTGAATCAG
66 GGCCTTGAATCAGCACAATGGCACCTT-A-CATCTTTAAGTCCAATATCACCGGCCTTGAATCAG
*
151620 CACATTGGCATCTTCATCTT
129 CACATTGGCATCTTCAACTT
* *
151640 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTAGCATCTTCATCATTAAGACCAATGTCGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTCATCATTAAGACCAATGTCGCT
* * **
151705 GGCCTTGAATCAGCACAATGGCACCTT-CATCTTTAAGTCCGATATTATTGGCCTTGAATCAGCA
66 GGCCTTGAATCAGCACAATGGCACCTTACATCTTTAAGTCCAATATCACCGGCCTTGAATCAGCA
* *
151769 TATTGGCATCTTTAACATT
131 CATTGGCATCTTCAAC-TT
*
151788 CCTAAGTCCAATGTCGCTGGCCTTG
1 --TAAGTCCAATATCGCTGGCCTTG
151813 TCTCAGCACA
Statistics
Matches: 149, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
147 43 0.29
148 2 0.01
150 104 0.70
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (148 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTCATCATTAAGACCAATGTCGCT
GGCCTTGAATCAGCACAATGGCACCTTACATCTTTAAGTCCAATATCACCGGCCTTGAATCAGCA
CATTGGCATCTTCAACTT
Found at i:152630 original size:21 final size:19
Alignment explanation
Indices: 152604--152656 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
152594 TTCAATAATT
152604 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* * *
152625 TGTATCGATTCATAAGTAT
1 TGTATCGATACAAAAGTAA
152644 TGTATCGATACAA
1 TGTATCGATACAA
152657 TGTATCGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.44
20 3 0.11
21 12 0.44
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:152662 original size:13 final size:13
Alignment explanation
Indices: 152644--152669 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
152634 TCATAAGTAT
152644 TGTATCGATACAA
1 TGTATCGATACAA
152657 TGTATCGATACAA
1 TGTATCGATACAA
152670 AAGCTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:152710 original size:40 final size:40
Alignment explanation
Indices: 152655--152748 Score: 179
Period size: 40 Copynumber: 2.4 Consensus size: 40
152645 GTATCGATAC
*
152655 AATGTATCGATACAAAAGCTACCTTGCATACTGCCAAGGA
1 AATGTATCGATACAAAAGCTACCCTGCATACTGCCAAGGA
152695 AATGTATCGATACAAAAGCTACCCTGCATACTGCCAAGGA
1 AATGTATCGATACAAAAGCTACCCTGCATACTGCCAAGGA
152735 AATGTATCGATACA
1 AATGTATCGATACA
152749 TTATTCAATG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (40 bp):
AATGTATCGATACAAAAGCTACCCTGCATACTGCCAAGGA
Found at i:152760 original size:20 final size:20
Alignment explanation
Indices: 152735--152810 Score: 152
Period size: 20 Copynumber: 3.8 Consensus size: 20
152725 CTGCCAAGGA
152735 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
152755 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
152775 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
152795 AATGTATCGATACATT
1 AATGTATCGATACATT
152811 GTATCGATAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:152815 original size:13 final size:13
Alignment explanation
Indices: 152797--152823 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
152787 CATTATTCAA
152797 TGTATCGATACAT
1 TGTATCGATACAT
152810 TGTATCGATACAT
1 TGTATCGATACAT
152823 T
1 T
152824 AATCTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:152819 original size:33 final size:33
Alignment explanation
Indices: 152777--152842 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
152767 CATTATTCAA
*
152777 TGTATCGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTAATCAATGTATCGATACAT
**
152810 TGTATCGATACATTAATCTTTGTATCGATACAT
1 TGTATCGATACATTAATCAATGTATCGATACAT
152843 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTAATCAATGTATCGATACAT
Found at i:158465 original size:16 final size:15
Alignment explanation
Indices: 158441--158471 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
158431 AAAGGCTTTC
158441 AAAAATTTTAATAGA
1 AAAAATTTTAATAGA
158456 AAAAAGTTTTAATAGA
1 AAAAA-TTTTAATAGA
158472 GGAAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (15 bp):
AAAAATTTTAATAGA
Found at i:159843 original size:20 final size:21
Alignment explanation
Indices: 159818--159857 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
159808 ATTTTTTCGG
*
159818 GATGTATTGATACAT-TGAAT
1 GATGTATCGATACATCTGAAT
159838 GATGTATCGATACATCTGAA
1 GATGTATCGATACATCTGAA
159858 AAAACCCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (21 bp):
GATGTATCGATACATCTGAAT
Found at i:159905 original size:13 final size:13
Alignment explanation
Indices: 159887--159926 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
159877 ACAATGTTTT
159887 TTGTATCGATACA
1 TTGTATCGATACA
*
159900 TTGTATTGATACA
1 TTGTATCGATACA
*
159913 ATGTATCGATACA
1 TTGTATCGATACA
159926 T
1 T
159927 GGGTTACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:164987 original size:7 final size:7
Alignment explanation
Indices: 164974--165007 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
164964 AAATTAGGAG
164974 AAATTTA
1 AAATTTA
*
164981 CAATTTA
1 AAATTTA
*
164988 CAATTTA
1 AAATTTA
164995 AAATTTA
1 AAATTTA
165002 AAATTT
1 AAATTT
165008 GTTTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:165317 original size:11 final size:11
Alignment explanation
Indices: 165301--165336 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
165291 GAAATTTTTG
165301 AAAATAAAAAT
1 AAAATAAAAAT
165312 AAAAT-AAAAT
1 AAAATAAAAAT
165322 AAAATAATAAAT
1 AAAATAA-AAAT
165334 AAA
1 AAA
165337 TATGACTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.43
11 6 0.26
12 7 0.30
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:168621 original size:21 final size:21
Alignment explanation
Indices: 168597--168673 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
168587 ATTACAGCTC
168597 ATTGTATTGATACATGTCAGG
1 ATTGTATTGATACATGTCAGG
* *
168618 ATTGTATCGATACATGTCAAG
1 ATTGTATTGATACATGTCAGG
* *
168639 ATTGTGTTAATACATGAT-AGG
1 ATTGTATTGATACATG-TCAGG
*
168660 ATTGTATGGATACA
1 ATTGTATTGATACA
168674 ATTAAGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
21 45 0.98
22 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.36
Consensus pattern (21 bp):
ATTGTATTGATACATGTCAGG
Found at i:173755 original size:18 final size:18
Alignment explanation
Indices: 173732--173775 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
173722 TCTAATATGA
*
173732 AAAATTATCAAGCTAAAT-
1 AAAATTAAC-AGCTAAATC
*
173750 AAAATTAACAGCTTAATC
1 AAAATTAACAGCTAAATC
173768 AAAATTAA
1 AAAATTAA
173776 TTAGTCTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAATTAACAGCTAAATC
Found at i:179404 original size:22 final size:23
Alignment explanation
Indices: 179376--179431 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
179366 TGGACATGTT
179376 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
179398 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
179421 AAAAATGCATG
1 AAAAATGCATG
179432 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:180389 original size:20 final size:20
Alignment explanation
Indices: 180342--180415 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
180332 AAAAGGACAT
*
180342 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
180361 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
180382 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
180402 AATGTATCGATACA
1 AATGTATCGATACA
180416 ACAGGGTATG
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:180410 original size:40 final size:39
Alignment explanation
Indices: 180339--180415 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
180329 GGTAAAAGGA
* *
180339 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
180378 CATACATGTATCGATATATTGAAAAATGTATCGATACA
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACA
180416 ACAGGGTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:181284 original size:29 final size:29
Alignment explanation
Indices: 180891--182076 Score: 1647
Period size: 29 Copynumber: 41.2 Consensus size: 29
180881 ACAATGGTGA
* * *
180891 TTTGAAAAGGGTTACCATTGACTTGCATGGGC
1 TTTGAAAAGAG-TGCCACTGACTTG--TGGGC
* *
180923 TTT-AAAAGGGTGCCACTGACGTGCGTGGGC
1 TTTGAAAAGAGTGCCACTGAC-T-TGTGGGC
* * *
180953 TTTG-AAAGAATGCCACTAACTCGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
180981 TTTGAAAGGA-TGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
181009 TTTG-AAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
181037 TTTGAAAAG-GTACCACTAACTTGCGTGAGC
1 TTTGAAAAGAGTGCCACTGACTT--GTGGGC
181067 TTT-AAAAGGAGTGCCACTGACTTGTGTGAGC
1 TTTGAAAA-GAGTGCCACTGACTTGTG-G-GC
*
181098 TTT-AAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181126 TTTG-AAAGAGTGCCACTGAATTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
181154 TTCG-CAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181182 TTCG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
181210 TCT-AAAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181238 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181266 TTTGAAAAGAGCGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
181295 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181324 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * * *
181353 TTTG-AAAGGGTGCCATTGACTTATGGTC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181381 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
181410 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181439 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181468 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181496 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181525 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
181553 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181582 TTTGAAAAG-GTGCCACTGACTTATGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181610 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181639 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181667 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
181696 TTTGAAAAG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181724 TTTGAAAAGAGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181753 TTTGAAAAGAGTGCCACTGATTTTTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
181782 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181811 TTTGAAAGGAGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181840 TTTG-AAAGGGTGCCACTGAGTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181868 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181896 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
181925 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181954 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181983 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
182012 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
182041 TTTAAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
182070 TTTGAAA
1 TTTGAAA
182077 GGGATGAACA
Statistics
Matches: 1041, Mismatches: 90, Indels: 49
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.00
28 398 0.38
29 552 0.53
30 55 0.05
31 28 0.03
32 4 0.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TTTGAAAAGAGTGCCACTGACTTGTGGGC
Found at i:181301 original size:57 final size:57
Alignment explanation
Indices: 180891--182076 Score: 1657
Period size: 57 Copynumber: 20.6 Consensus size: 57
180881 ACAATGGTGA
* * * *
180891 TTTGAAAAGGGTTACCATTGACTTGCATGGGCTTT-AAAAGGGTGCCACTGACGTGCGTGGGC
1 TTTG-AAAGGG-TGCCACTGACTTG--TGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGC
** * * *
180953 TTTGAAAGAATGCCACTAACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * * *
181009 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTACCACTAACTTGCGTGAGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGC
* *
181067 TTTAAAAGGAGTGCCACTGACTTGTGTGAGCTTT-AAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTG-G-GCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * * * *
181126 TTTGAAAGAGTGCCACTGAATTGTGGGCTTCG-CAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * * *
181182 TTCGAAAGGGTGCCACTGACTTGTGGGCTCT-AAAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181238 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGCGCCACTGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181295 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * * *
181353 TTTGAAAGGGTGCCATTGACTTATGGTCTTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181410 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181468 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181525 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
181582 TTTGAAAAGGTGCCACTGACTTATGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181639 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181696 TTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
181753 TTTGAAAAGAGTGCCACTGATTTTTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
181811 TTTGAAAGGAGTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGAGTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181868 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
181925 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
181983 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
182041 TTTAAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
1 TTT-GAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
182077 GGGATGAACA
Statistics
Matches: 1014, Mismatches: 91, Indels: 42
0.88 0.08 0.04
Matches are distributed among these distances:
56 175 0.17
57 414 0.41
58 350 0.35
59 36 0.04
60 15 0.01
61 20 0.02
62 4 0.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (57 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
Found at i:183315 original size:1 final size:1
Alignment explanation
Indices: 183311--183362 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
183301 TTTTTTGCTA
* * * * * *
183311 TTTTTTCTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTTGTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
183363 GGGTGTAAAG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:183323 original size:20 final size:18
Alignment explanation
Indices: 183298--183361 Score: 67
Period size: 17 Copynumber: 3.5 Consensus size: 18
183288 GACCCTTCTA
183298 TTTTTTTTTGCTATTTTTTC
1 TTTTTTTTTG-T-TTTTTTC
*
183318 TTTTTTTTTGTTTTTTTG
1 TTTTTTTTTGTTTTTTTC
* * *
183336 TTTTGTTTT-TTTTTGTG
1 TTTTTTTTTGTTTTTTTC
183353 TTTTTTTTT
1 TTTTTTTTT
183362 TGGGTGTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.38
18 14 0.35
19 1 0.03
20 10 0.25
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTGTTTTTTTC
Found at i:183334 original size:13 final size:13
Alignment explanation
Indices: 183318--183362 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
183308 CTATTTTTTC
183318 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
*
183331 TTTTGTTTTG-TT
1 TTTTTTTTTGTTT
*
183343 TTTTTTTGTGTTT
1 TTTTTTTTTGTTT
183356 TTTTTTT
1 TTTTTTT
183363 GGGTGTAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:183349 original size:10 final size:10
Alignment explanation
Indices: 183298--183360 Score: 63
Period size: 10 Copynumber: 5.9 Consensus size: 10
183288 GACCCTTCTA
183298 TTTTTTTTTG
1 TTTTTTTTTG
* * *
183308 CTATTTTTTC
1 TTTTTTTTTG
183318 TTTTTTTTTG
1 TTTTTTTTTG
183328 TTTTTTTGTTTTG
1 --TTTTT-TTTTG
183341 TTTTTTTTTG
1 TTTTTTTTTG
183351 TGTTTTTTTT
1 T-TTTTTTTT
183361 TTGGGTGTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
10 20 0.47
11 13 0.30
12 5 0.12
13 5 0.12
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:183361 original size:12 final size:12
Alignment explanation
Indices: 183318--183361 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
183308 CTATTTTTTC
183318 TTTTTTTTTGT-
1 TTTTTTTTTGTG
183329 TTTTTTGTTT-TG
1 TTTTTT-TTTGTG
183341 TTTTTTTTTGTG
1 TTTTTTTTTGTG
183353 TTTTTTTTT
1 TTTTTTTTT
183362 TGGGTGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTGTG
Found at i:183363 original size:23 final size:22
Alignment explanation
Indices: 183311--183363 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
183301 TTTTTTGCTA
*
183311 TTTTTTCTTTTTTTTTGTTTTT
1 TTTTTTGTTTTTTTTTGTTTTT
183333 TTGTTTTGTTTTTTTTTGTGTTTT
1 TT-TTTTGTTTTTTTTTGT-TTTT
183357 TTTTTTG
1 TTTTTTG
183364 GGTGTAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 2 0.07
23 20 0.71
24 6 0.21
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (22 bp):
TTTTTTGTTTTTTTTTGTTTTT
Done.