Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2077
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: 194399
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:166407 original size:115 final size:114
Alignment explanation
Indices: 166206--166664 Score: 629
Period size: 115 Copynumber: 4.0 Consensus size: 114
166196 CGTTCATCTC
* *
166206 TTCAAAGCCCACAAGTTAATGGCA-CTCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTTAGTGGCATCT-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
* * * *
166270 CCCACAAGTCAGTGACACCCTTTCAAA-CACCACAAAATCAGTGGCA-TCCT
65 CCCACAAGTCAGTGGCACCCTTTCAAAGC-CCAC-AAGTTAGTGGCACTCTT
* * * *
166320 TTCAAACCCCACAAAATCAGTGGCATCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAG
1 TTCAAAGCCCAC-AAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
* *
166385 CCCACAAGTCAGAGGCACCCTTTTAAAGCCCACAAGTTAGTGGCACTCTT
65 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
*
166435 TTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAATGGCAC-CTTTTCAAAGC
1 TTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
166499 CCACGCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
66 CCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
* *
166550 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
166615 CCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCA
66 CCACA--AGTCAGTGGC-AC-CCTTTCAAAG-CC-CACAAGTTAGTGGCA
166665 TCATTTTTTT
Statistics
Matches: 308, Mismatches: 24, Indels: 20
0.88 0.07 0.06
Matches are distributed among these distances:
113 14 0.05
114 60 0.19
115 180 0.58
116 26 0.08
117 2 0.01
118 9 0.03
119 2 0.01
120 15 0.05
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (114 bp):
TTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
Found at i:166514 original size:172 final size:171
Alignment explanation
Indices: 166206--166651 Score: 619
Period size: 172 Copynumber: 2.6 Consensus size: 171
166196 CGTTCATCTC
*
166206 TTCAAAGCCCACAAGTTA-ATGGCACTCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTTAGA-GGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAG
* * * *
166270 CCCACAAGTCAGTGACACCCTTTCAAA-CACCACAAAATCAGTGGCATCCTTTCAAACCCCACAA
65 CCCACAAGTCAGTGGCATCTTTTCAAAGC-CCAC-AAATCAATGGCATCCTTTCAAACCCCACAA
* *
166334 AATCAGTGGCATCTTTTCAAAGCCCACAAATCAGTGGCACTCTT
128 AATCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCTT
* *
166378 TTCAAAGCCCACAAGTCAGAGGCACCCTTTTAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTTAGAGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
* * * *
166443 CCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAATGGCA-CCTTTTCAAAGCCCACGCAA
66 CCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAATCAATGGCATCC-TTTCAAACCCCAC-AAA
* * *
166507 GTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
129 ATCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCTT
* *
166550 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTTAGAGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
*
166615 CCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACA
66 CCACA--AGTCAGTGGC-A-TCTTTTCAAAGCCCACA
166652 CAAGTTAGTG
Statistics
Matches: 244, Mismatches: 22, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
170 2 0.01
171 22 0.09
172 192 0.79
173 2 0.01
174 8 0.03
175 1 0.00
176 17 0.07
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (171 bp):
TTCAAAGCCCACAAGTTAGAGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
CCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAATCAATGGCATCCTTTCAAACCCCACAAAAT
CAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCTT
Found at i:166797 original size:45 final size:48
Alignment explanation
Indices: 166733--166852 Score: 129
Period size: 49 Copynumber: 2.5 Consensus size: 48
166723 CTATCTGACA
* * *
166733 TCGCTAGCATTGAATCAGCATATTGG-C-ACCTTTA-TTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGTCTACCTTTACTTAGCCCAATG
* *
166778 TCGCTGGCCTTGAATCAGCACATTGGTCTACTTTTACCTTAGTCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGTCTACCTTTA-CTTAGCCCAATG
** **
166827 TTACTGGCCTTGAATTGGCACATTGG
1 TCGCTGGCCTTGAATCAGCACATTGG
166853 CAATCCTCTA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 23 0.37
46 1 0.02
47 6 0.10
49 32 0.52
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (48 bp):
TCGCTGGCCTTGAATCAGCACATTGGTCTACCTTTACTTAGCCCAATG
Found at i:167258 original size:20 final size:20
Alignment explanation
Indices: 167230--167301 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
167220 TTTTACCCAG
167230 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
167250 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
167270 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
167290 ATGTATCGATAC
1 ATGTATCGATAC
167302 TGTAGACATC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:167274 original size:40 final size:39
Alignment explanation
Indices: 167230--167305 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 39
167220 TTTTACCCAG
*
167230 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATAC-TGTATGA
*
167270 ATGTATCGATACATTCTTCAATGTATCGATACTGTA
1 ATGTATCGATACATTCTTCAATATATCGATACTGTA
167306 GACATCCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACTGTATGA
Found at i:179684 original size:20 final size:19
Alignment explanation
Indices: 179657--179794 Score: 114
Period size: 20 Copynumber: 6.8 Consensus size: 19
179647 TAAAAGGACA
*
179657 AAATGTATCGATACATTCG
1 AAATGTATCGATACATTAG
* * *
179676 TACATGTATCAATACATTAA
1 -AAATGTATCGATACATTAG
*
179696 AAGATGTATCGATACATCTGGG
1 AA-ATGTATCGATACAT-T-AG
*
179718 TAATGTATCGATACATTAG
1 AAATGTATCGATACATTAG
* *
179737 AAGATGTATCCATACATCTGGG
1 AA-ATGTATCGATACAT-T-AG
* *
179759 TAATGTATCGATACATTGAA
1 AAATGTATCGATACATT-AG
179779 AAATGTATCGATACAT
1 AAATGTATCGATACAT
179795 CTAGGTAAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
19 3 0.03
20 59 0.63
21 29 0.31
22 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (19 bp):
AAATGTATCGATACATTAG
Found at i:179725 original size:21 final size:21
Alignment explanation
Indices: 179699--179802 Score: 115
Period size: 20 Copynumber: 5.0 Consensus size: 21
179689 ACATTAAAAG
179699 ATGTATCGATACATCTGGGTA
1 ATGTATCGATACATCTGGGTA
* *
179720 ATGTATCGATACAT-T-AGAA
1 ATGTATCGATACATCTGGGTA
*
179739 GATGTATCCATACATCTGGGTA
1 -ATGTATCGATACATCTGGGTA
***
179761 ATGTATCGATACAT-TGAAAA
1 ATGTATCGATACATCTGGGTA
*
179781 ATGTATCGATACATCTAGGTA
1 ATGTATCGATACATCTGGGTA
179802 A
1 A
179803 AAATGTGACT
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.03
20 31 0.47
21 31 0.47
22 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATCTGGGTA
Found at i:179734 original size:41 final size:41
Alignment explanation
Indices: 179659--179802 Score: 204
Period size: 41 Copynumber: 3.5 Consensus size: 41
179649 AAAGGACAAA
* *
179659 ATGTATCGATACAT-T-CGTACATGTATCAATACATTAAAAG
1 ATGTATCGATACATCTGGGTA-ATGTATCGATACATTAAAAG
*
179699 ATGTATCGATACATCTGGGTAATGTATCGATACATTAGAAG
1 ATGTATCGATACATCTGGGTAATGTATCGATACATTAAAAG
*
179740 ATGTATCCATACATCTGGGTAATGTATCGATACATTGAAAA-
1 ATGTATCGATACATCTGGGTAATGTATCGATACATT-AAAAG
*
179781 ATGTATCGATACATCTAGGTAA
1 ATGTATCGATACATCTGGGTAA
179803 AAATGTGACT
Statistics
Matches: 94, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
40 14 0.15
41 74 0.79
42 6 0.06
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (41 bp):
ATGTATCGATACATCTGGGTAATGTATCGATACATTAAAAG
Found at i:179784 original size:61 final size:61
Alignment explanation
Indices: 179656--179794 Score: 156
Period size: 61 Copynumber: 2.3 Consensus size: 61
179646 GTAAAAGGAC
* * *
179656 AAAATGTATCGATACATTCGTACATGTATCAATACATTAAAAGATGTATCGATACATCTGG
1 AAAATGTATCGATACATTAGAACATGTATCAATACATTAAAAGATGTATCGATACATCTGA
** * * ***
179717 GTAATGTATCGATACATTAGAAGATGTATCCATACATCTGGGTA-ATGTATCGATACAT-TGA
1 AAAATGTATCGATACATTAGAACATGTATCAATACAT-T-AAAAGATGTATCGATACATCTGA
179778 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
179795 CTAGGTAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
61 48 0.75
62 15 0.23
63 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (61 bp):
AAAATGTATCGATACATTAGAACATGTATCAATACATTAAAAGATGTATCGATACATCTGA
Found at i:182437 original size:24 final size:24
Alignment explanation
Indices: 182391--182437 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
182381 CTTAATTAAT
* *
182391 AAAAAATAAAAAAAATTAGAAATC
1 AAAAAATAAAAAAAATAAAAAATC
* *
182415 AAAAAATAATAATAATAAAAAAT
1 AAAAAATAAAAAAAATAAAAAAT
182438 GACTAATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (24 bp):
AAAAAATAAAAAAAATAAAAAATC
Found at i:182455 original size:9 final size:9
Alignment explanation
Indices: 182387--182464 Score: 56
Period size: 9 Copynumber: 8.7 Consensus size: 9
182377 ATTTCTTAAT
182387 TAATAAAAAA
1 TAAT-AAAAA
182397 TAA-AAAAA
1 TAATAAAAA
* *
182405 -ATTAGAAA
1 TAATAAAAA
*
182413 TCA-AAAAA
1 TAATAAAAA
*
182421 TAATAATAA
1 TAATAAAAA
182430 TAA-AAAATGA
1 TAATAAAA--A
182440 CTAATAAAAA
1 -TAATAAAAA
182450 TAATAAAAA
1 TAATAAAAA
182459 TAATAA
1 TAATAA
182465 TAAAAGAGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
7 1 0.02
8 18 0.34
9 22 0.42
10 5 0.09
11 3 0.06
12 4 0.08
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (9 bp):
TAATAAAAA
Found at i:183161 original size:35 final size:35
Alignment explanation
Indices: 183114--183251 Score: 197
Period size: 35 Copynumber: 3.9 Consensus size: 35
183104 GCACGAACGG
*
183114 CAGCTTCTAGCCACGAACACCGGTAGCAGCTCCAT
1 CAGCTTCTAGCCACGAACACCGGCAGCAGCTCCAT
* *
183149 TAGCTTCTAGCCATGAACACCGGCAGCAGCTCCAT
1 CAGCTTCTAGCCACGAACACCGGCAGCAGCTCCAT
*
183184 CAGCTTCTAGCCACGAACACCGGCAGTAGCTCCAT
1 CAGCTTCTAGCCACGAACACCGGCAGCAGCTCCAT
* *
183219 CAGCTTCCAACCCATC-AACACCGGCAGCAGCTC
1 CAGCTT-CTAGCCA-CGAACACCGGCAGCAGCTC
183252 TACAACCTTC
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
35 70 0.76
36 21 0.23
37 1 0.01
ACGTcount: A:0.26, C:0.38, G:0.19, T:0.17
Consensus pattern (35 bp):
CAGCTTCTAGCCACGAACACCGGCAGCAGCTCCAT
Found at i:191343 original size:42 final size:42
Alignment explanation
Indices: 191292--192042 Score: 796
Period size: 42 Copynumber: 17.8 Consensus size: 42
191282 TTTTTGTTTT
** *
191292 CCCTTAGTCTATCTGTTGGCTTTGACCCTGGAGACTTTTCAA
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* * *
191334 CCCTTAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTTTAT
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* * * *
191376 CCCTCAGTCTGCCTGTCGGCTTTGTCCCTGGAGACTTTCCTAT
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-AA
*
191419 CCCTTAGTCTACCTGTCGGCTTTGACCCTGGAGACTTTTCAA
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
*
191461 CCCTTAGTTTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* *
191503 CCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCAT
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
*
191545 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* * *
191587 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGGGACTTTCCTA
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* * *
191629 CCCTTCAGTCTGCCTGTCGGCTTTGACTCTGGGGAC-TTTCTTA
1 CCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-AA
* **
191672 CCCTTCAGTCTGCCTGTCGGCTTTGACTCTGGAGACTGCCTC-A
1 CCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTTCAA
* * * * *
191715 --TTTAAAGTCTACTTGTCGGCTTTGACCTTGGAGACTTTTCAT
1 CCCTT--AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* * * * **
191757 CTCTTAGTCTGCCTGTTGGTTTTGACCCTGGAAACTTTTCTT
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* *
191799 CCCTTAGTTTACCTGTCGGCTTTGACCCTGGAGACTTTTCAA
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* ** *
191841 CCCTTAGTCTGCCTGTCGACTTTGACCCTAAAGACTTTTCAT
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* * * **
191883 CCCTTAATTTGCCTGTCGG-TTTAACCCTGGAGAC-TTTCTTT
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-AA
* * * * * **
191924 CCCTCAATCTGCCTGTCGGTTTTGACCTTGGAGACTTTCCTT
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* * * **
191966 CTCTCAGTCTGCCTGTCGGCTTT-ATCCCTTGAGACTTTTCTTT
1 CCCTTAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTTC-AA
* * * * *
192009 CCCTAAGTCTGCCCGTTGGTTTTGACCCGGGAGA
1 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGA
192043 ATATTTTCTT
Statistics
Matches: 605, Mismatches: 89, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
40 4 0.01
41 35 0.06
42 426 0.70
43 135 0.22
44 3 0.00
45 2 0.00
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.37
Consensus pattern (42 bp):
CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
Found at i:192052 original size:254 final size:252
Alignment explanation
Indices: 191290--192052 Score: 921
Period size: 254 Copynumber: 3.0 Consensus size: 252
191280 CTTTTTTGTT
* * *
191290 TTCCCTTAGTCTATCTGTTGGCTTTGACCCTGGAGACTTTTCAACCCTTAGTCTGCCTATCGGCT
1 TTCCCTTAGTCTACCTGTCGGCTTTGACCCTGGAGACTTTTCAACCCTTAGTCTGCCTGTCGGCT
* * * *
191355 TTGACCCTGGAGACTTTTTATCCCTCAGTCTGCCTGTCGGCTTTGTCCCTGGAGACTTTCCTATC
66 TTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-CTTTC
* * * ** * * *
191420 CCTTAGTCTACCTGTCGGCTTTGACCCTGGAGACTTTTCAACCCTTAGTTTGCCTGTCGGCTTTG
130 CCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TTTCCTCTCTAAGTCTGCCTGTCGGCTTTG
* * * * *
191485 ACCCTGGAGACTTTTCAACCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAG-ACTTTTC
194 ACCCTTGAGACTTTTCATCCCTTAGTCTGCCTGTTGGTTTTGACCCTGGAGAACTTTTC
* * *
191543 ATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAACCCTTAGTCTGCCTGTCGGCT
1 TTCCCTTAGTCTACCTGTCGGCTTTGACCCTGGAGACTTTTCAACCCTTAGTCTGCCTGTCGGCT
* * * * *
191608 TTGACCCTGGGGAC-TTTCCTACCCTTCAGTCTGCCTGTCGGCTTTGACTCTGGGGACTTTCTTA
66 TTGACCCTGGAGACTTTTCAT-CCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTT
* * * *
191672 CCCTTCAGTCTGCCTGTCGGCTTTGA-CTCTGGAGAC-TGCCTCATTTAAAGTCTACTTGTCGGC
129 CCC-TCAGTCTGCCTGTCGGCTTTGACCT-TGGAGACTTTCCTC-TCT-AAGTCTGCCTGTCGGC
*
191735 TTTGA-CCTTGGAGACTTTTCATCTCTTAGTCTGCCTGTTGGTTTTGACCCTGGA-AACTTTTC
190 TTTGACCCTT-GAGACTTTTCATCCCTTAGTCTGCCTGTTGGTTTTGACCCTGGAGAACTTTTC
* *
191797 TTCCCTTAGTTTACCTGTCGGCTTTGACCCTGGAGACTTTTCAACCCTTAGTCTGCCTGTCGACT
1 TTCCCTTAGTCTACCTGTCGGCTTTGACCCTGGAGACTTTTCAACCCTTAGTCTGCCTGTCGGCT
** * * *
191862 TTGACCCTAAAGACTTTTCATCCCTTAATTTGCCTGTCGG-TTTAACCCTGGAGACTTTCTTTCC
66 TTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTTCC
* * *
191926 CTCAATCTGCCTGTCGGTTTTGACCTTGGAGACTTTCCTTCTCTCAGTCTGCCTGTCGGCTTT-A
131 CTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCC-TCTCTAAGTCTGCCTGTCGGCTTTGA
* * * * *
191990 TCCCTTGAGACTTTTCTTTCCCTAAGTCTGCCCGTTGGTTTTGACCCGGGAGAATATTTTC
195 -CCCTTGAGACTTTTC-ATCCCTTAGTCTGCCTGTTGGTTTTGACCCTGGAGAA-CTTTTC
192051 TT
1 TT
192053 TTTTGCTTAC
Statistics
Matches: 432, Mismatches: 61, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
250 1 0.00
251 53 0.12
252 68 0.16
253 102 0.24
254 203 0.47
255 5 0.01
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.37
Consensus pattern (252 bp):
TTCCCTTAGTCTACCTGTCGGCTTTGACCCTGGAGACTTTTCAACCCTTAGTCTGCCTGTCGGCT
TTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTTCC
CTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTCTCTAAGTCTGCCTGTCGGCTTTGAC
CCTTGAGACTTTTCATCCCTTAGTCTGCCTGTTGGTTTTGACCCTGGAGAACTTTTC
Found at i:192542 original size:18 final size:17
Alignment explanation
Indices: 192480--192555 Score: 56
Period size: 18 Copynumber: 4.8 Consensus size: 17
192470 TTTGATAATA
192480 AAATAA-AAAAATCAA-
1 AAATAATAAAAATCAAG
* *
192495 AAA-AA-AATAATTAA-
1 AAATAATAAAAATCAAG
* * *
192509 AAATAATAATATTCAAT
1 AAATAATAAAAATCAAG
192526 ATAATAATAAAAATCAAG
1 A-AATAATAAAAATCAAG
192544 AAATAA-AAAAAT
1 AAATAATAAAAAT
192556 TCAAAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.24
15 5 0.10
16 13 0.26
17 6 0.12
18 14 0.28
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.22
Consensus pattern (17 bp):
AAATAATAAAAATCAAG
Found at i:192664 original size:35 final size:35
Alignment explanation
Indices: 192618--192790 Score: 296
Period size: 35 Copynumber: 4.9 Consensus size: 35
192608 AAAAGAAAAC
192618 AAGGCATGGAATGATGGGCATGGAATAAAAAAATG
1 AAGGCATGGAATGATGGGCATGGAATAAAAAAATG
*
192653 AAGACATGGAATGATGGGCATGGAATAAAAAAATG
1 AAGGCATGGAATGATGGGCATGGAATAAAAAAATG
192688 AAGGCATGGAATGATGGGCATGGAAT-AAAAAATG
1 AAGGCATGGAATGATGGGCATGGAATAAAAAAATG
192722 AAGGCATGGAATGATGGGCATGGAAT-AAAAAATG
1 AAGGCATGGAATGATGGGCATGGAATAAAAAAATG
*
192756 CTAGGCATGGAATGATGGGCATGGAATAAATAAAA
1 -AAGGCATGGAATGATGGGCATGGAATAAA-AAAA
192791 AGAAAGAAGA
Statistics
Matches: 132, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
34 42 0.32
35 84 0.64
36 2 0.02
37 4 0.03
ACGTcount: A:0.45, C:0.06, G:0.31, T:0.18
Consensus pattern (35 bp):
AAGGCATGGAATGATGGGCATGGAATAAAAAAATG
Found at i:192694 original size:21 final size:20
Alignment explanation
Indices: 192669--192768 Score: 71
Period size: 14 Copynumber: 5.5 Consensus size: 20
192659 TGGAATGATG
192669 GGCATGGAATAAAAAAATGAA
1 GGCATGGAAT-AAAAAATGAA
*
192690 GGCATGGAAT----GATG--
1 GGCATGGAATAAAAAATGAA
192704 GGCATGGAATAAAAAATGAA
1 GGCATGGAATAAAAAATGAA
*
192724 GGCATGGAAT----GATG--
1 GGCATGGAATAAAAAATGAA
*
192738 GGCATGGAATAAAAAATGCTA
1 GGCATGGAATAAAAAATG-AA
192759 GGCATGGAAT
1 GGCATGGAAT
192769 GATGGGCATG
Statistics
Matches: 62, Mismatches: 4, Indels: 26
0.67 0.04 0.28
Matches are distributed among these distances:
14 20 0.32
16 6 0.10
18 6 0.10
20 10 0.16
21 20 0.32
ACGTcount: A:0.44, C:0.07, G:0.31, T:0.18
Consensus pattern (20 bp):
GGCATGGAATAAAAAATGAA
Found at i:192746 original size:69 final size:69
Alignment explanation
Indices: 192617--192785 Score: 295
Period size: 69 Copynumber: 2.4 Consensus size: 69
192607 AAAAAGAAAA
192617 CAAGGCATGGAATGATGGGCATGGAATAAAAAAATGAAGACATGGAATGATGGGCATGGAATAAA
1 CAAGGCATGGAATGATGGGCATGGAAT-AAAAAATGAAGACATGGAATGATGGGCATGGAAT-AA
192682 AAAATG
64 AAAATG
*
192688 -AAGGCATGGAATGATGGGCATGGAATAAAAAATGAAGGCATGGAATGATGGGCATGGAATAAAA
1 CAAGGCATGGAATGATGGGCATGGAATAAAAAATGAAGACATGGAATGATGGGCATGGAATAAAA
192752 AATG
66 AATG
*
192756 CTAGGCATGGAATGATGGGCATGGAATAAA
1 CAAGGCATGGAATGATGGGCATGGAATAAA
192786 TAAAAAGAAA
Statistics
Matches: 95, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
68 8 0.08
69 61 0.64
70 26 0.27
ACGTcount: A:0.44, C:0.07, G:0.31, T:0.18
Consensus pattern (69 bp):
CAAGGCATGGAATGATGGGCATGGAATAAAAAATGAAGACATGGAATGATGGGCATGGAATAAAA
AATG
Found at i:193730 original size:15 final size:15
Alignment explanation
Indices: 193710--193739 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
193700 AAGTGCAAAG
193710 CAAAAAAATAAAAAA
1 CAAAAAAATAAAAAA
193725 CAAAAAAATAAAAAA
1 CAAAAAAATAAAAAA
193740 ATGAAACGAA
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:0.87, C:0.07, G:0.00, T:0.07
Consensus pattern (15 bp):
CAAAAAAATAAAAAA
Found at i:193808 original size:15 final size:15
Alignment explanation
Indices: 193788--193819 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
193778 CATAACCAGA
193788 TGGATCTTTTTCTCT
1 TGGATCTTTTTCTCT
193803 TGGATCTTTTTCTCT
1 TGGATCTTTTTCTCT
193818 TG
1 TG
193820 TTTAGATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.19, G:0.16, T:0.59
Consensus pattern (15 bp):
TGGATCTTTTTCTCT
Done.