Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold278
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: 230431
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:192484 original size:29 final size:29
Alignment explanation
Indices: 192452--192532 Score: 162
Period size: 29 Copynumber: 2.8 Consensus size: 29
192442 TGAGCTTATT
192452 ATTTCTTGTTTGTACAAATTCTTAGAGGC
1 ATTTCTTGTTTGTACAAATTCTTAGAGGC
192481 ATTTCTTGTTTGTACAAATTCTTAGAGGC
1 ATTTCTTGTTTGTACAAATTCTTAGAGGC
192510 ATTTCTTGTTTGTACAAATTCTT
1 ATTTCTTGTTTGTACAAATTCTT
192533 TGTCTAGATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (29 bp):
ATTTCTTGTTTGTACAAATTCTTAGAGGC
Found at i:193103 original size:67 final size:67
Alignment explanation
Indices: 192924--194142 Score: 606
Period size: 67 Copynumber: 18.5 Consensus size: 67
192914 CAAATGTCAC
* * * * * *
192924 TCAAC-CCTATTTCAACGTAGGTTTTA-CCTAAGTTACTTTTAGTTGACTTTATTGGTTTTGCCC
1 TCAACACCTTTTTCGACTTAGGTTTCATCCT-AGTCACTTTTAGTTGACTTTATTAGTTTTGCCC
192987 TAG
65 TAG
* * * * * * * *
192990 TCAATA-CTCTTTTCGATTTAGGTTTC-GCGCTGGTCTCCTCTAGTTGACTTTATTAGTTTTGCG
1 TCAACACCT-TTTTCGACTTAGGTTTCATC-CTAGTCACTTTTAGTTGACTTTATTAGTTTTGCC
193053 CTAG
64 CTAG
* * * * * * *
193057 TCAATACCTTTTTTGACTTACGTTTCATCCTAGTCACTTTTTGTTGACTTTATCAATTTTGCCTT
1 TCAACACCTTTTTCGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGCCCT
*
193122 GG
66 AG
* * * * * * * * **
193124 TTAACACCCTTTTGGACTAAGGTTTTCCT-CTCATGTC-C-TTTGGTTGACTTTATCAATTTCAC
1 TCAACACCTTTTTCGACTTAGG-TTTCATCCT-A-GTCACTTTTAGTTGACTTTATTAGTTTTGC
*
193186 CTTAG
63 CCTAG
* * * **
193191 TCAATA-CTCTTTTCGACTTAAGCTTTGC--CCTAGTCTCTTTTAGTTGACTTTATTA-CCTTG-
1 TCAACACCT-TTTTCGACTT-AGGTTT-CATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGC
*
193251 ---GG
63 CCTAG
* ** * * *
193253 T-AACACTTTTTTTTACTTAGGTTTCATCCTAGTCATTTTTAGTTGAGTTTATCAGTTTTGCCCT
1 TCAACACCTTTTTCGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGCCCT
193317 -G
66 AG
* * * * * * *
193318 GCTAACACCCTTTTCGACTTAGGTTTCACCCTAGTCA-TCTTAAATTGACTTTATCAGTTTCG-C
1 TC-AACACCTTTTTCGACTTAGGTTTCATCCTAGTCACT-TTTAGTTGACTTTATTAGTTTTGCC
*
193381 CTGG
64 CTAG
* * * * * ** **
193385 CCAACA-C-----CAACTTAGGTTTCGTCCTAGTCACCTTTAGTTAACTTTATCGGTTTCACCCT
1 TCAACACCTTTTTCGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGCCCT
193444 AG
66 AG
* ** * * **
193446 TCAAC-TCTTTTTCGACTTAGGTTTCA-CTCTAACCACTTTAAGTTGACTTTATTGGTTTCACCC
1 TCAACACCTTTTTCGACTTAGGTTTCATC-CTAGTCACTTTTAGTTGACTTTATTAGTTTTGCCC
193509 TAG
65 TAG
* ** * * * * * * *
193512 TTAACACCTTTTTTTACTTAGGTTTCA-CTTGGTCTCCTTTAGTTGGCTTTA-TCGATTT-CACC
1 TCAACACCTTTTTCGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGC-CC
193574 TTAG
65 -TAG
* * * * * * *
193578 TTAACACCCTTTTCAACTTAGGTTTCATCCTAGTCACCTTTAGTTGACTTCATTGGTTTTACCCT
1 TCAACACCTTTTTCGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGCCCT
*
193643 TG
66 AG
* * ** * ** * * *
193645 TCAAC-CC-TTTTCAACTTAGG-TTCTGTTATAATTTCCTTTAGTTGTCTTTATTAGTTTTACCC
1 TCAACACCTTTTTCGACTTAGGTTTC-ATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGCCC
193707 TAG
65 TAG
* * * **
193710 TCAACAACTTTTTTGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTTGTTTTGATCT
1 TCAACACCTTTTTCGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGCCCT
193775 AG
66 AG
* * * ** * * *
193777 TTAACACCCTTTTCAACTTAGGTTTTTTCCTAGTCATTTTTAGTTAACTTTA-TCGATTTTGCCC
1 TCAACACCTTTTTCGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTAG-TTTTGCCC
193841 TAG
65 TAG
* * * * * * * * **
193844 CCAACACCCTTTTCAACTTAAGTTT--TGCCTTGGT-ATCCTTTAGTTTACTTTATCAGTTTCAC
1 TCAACACCTTTTTCGACTTAGGTTTCAT-CC-TAGTCA-CTTTTAGTTGACTTTATTAGTTTTGC
* *
193906 CTTGG
63 CCTAG
* * * * * ** *
193911 TCAACACCTTTTTTGACTTATGTATT-GTCCTAGTCAAC-TTTAGTTGATTTTATCAGTTTCACA
1 TCAACACCTTTTTCGACTTAGGT-TTCATCCTAGTC-ACTTTTAGTTGACTTTATTAGTTTTGCC
*
193974 TTAG
64 CTAG
* * * * *
193978 TTAATTA--TTTTT--ACTTAGGTTTCATCCTAGTCTCTTTTAGTTGATTTTATTTGTTTTGCCC
1 TCAA-CACCTTTTTCGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGCCC
194039 TAG
65 TAG
* * * *
194042 TCAATACCCTTTTT-GACTTAGGTTTTATCCTAGTCACTTTTAGTTGAC-TTATCAATTTTGCCC
1 TCAACA-CCTTTTTCGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGCCC
194105 TAG
65 TAG
* * *
194108 TCAATACC-CTTTCGACTTAAGTTTCA-CCTTAGTCA
1 TCAACACCTTTTTCGACTTAGGTTTCATCC-TAGTCA
194143 ACGCCCTTTT
Statistics
Matches: 889, Mismatches: 200, Indels: 129
0.73 0.16 0.11
Matches are distributed among these distances:
59 1 0.00
60 43 0.05
61 43 0.05
62 6 0.01
63 5 0.01
64 50 0.06
65 81 0.09
66 147 0.17
67 475 0.53
68 32 0.04
69 6 0.01
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (67 bp):
TCAACACCTTTTTCGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTAGTTTTGCCCT
AG
Found at i:193600 original size:133 final size:131
Alignment explanation
Indices: 193415--193655 Score: 306
Period size: 133 Copynumber: 1.8 Consensus size: 131
193405 GTCCTAGTCA
* * * *
193415 CCTTTAGTTAACTTTATCGGTTTCACCCTAGTCAACTCTTTTTCGACTTAGGTTTCA-CTCTAAC
1 CCTTTAGTTAACTTTATCGATTTCACCCTAGTCAACCCCTTTTCAACTTAGGTTTCATC-CTAAC
* *
193479 CA-CTTTAAGTTGACTTTATTGGTTTCACCCTAGTTAACACCTTTTTTTACTTAGGTTTCACTTG
65 CACCTTT-AGTTGACTTCATTGGTTTCACCCTAGTCAAC-CCTTTTTTTACTTAGGTTTCACTTG
193543 GTCT
128 GTCT
** * * **
193547 CCTTTAGTTGGCTTTATCGATTTCACCTTAGTTAACACCCTTTTCAACTTAGGTTTCATCCTAGT
1 CCTTTAGTTAACTTTATCGATTTCACCCTAGTCAAC-CCCTTTTCAACTTAGGTTTCATCCTAAC
* *
193612 CACCTTTAGTTGACTTCATTGGTTTTACCCTTGTCAACCCTTTT
65 CACCTTTAGTTGACTTCATTGGTTTCACCCTAGTCAACCCTTTT
193656 CAACTTAGGT
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
132 37 0.40
133 50 0.54
134 5 0.05
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.44
Consensus pattern (131 bp):
CCTTTAGTTAACTTTATCGATTTCACCCTAGTCAACCCCTTTTCAACTTAGGTTTCATCCTAACC
ACCTTTAGTTGACTTCATTGGTTTCACCCTAGTCAACCCTTTTTTTACTTAGGTTTCACTTGGTC
T
Found at i:193686 original size:132 final size:134
Alignment explanation
Indices: 193415--193800 Score: 344
Period size: 132 Copynumber: 2.9 Consensus size: 134
193405 GTCCTAGTCA
** * * *
193415 CCTTTAGTTAACTTTATCG-GTTTCACCCTAGTCAAC-TCTTTTTCGACTTAGGTTTCA-CTCTA
1 CCTTTAGTTGGCTTTAT-GAGTTTCACCCTAGTCAACAACCTTTTCAACTTAGGTTTCATC-CTA
** * * * ** *
193477 ACCA-CTTTAAGTTGACTTTATTGG-TTTCACCCTAGTTAACACCTTTTTTTACTTAGGTT-TCA
64 GTCACCTTT-AGTTGACTTCATTGGTTTTGA-CCTAGTTAACACCCTTTTCAACTTAGGTTCT-G
* ** *
193539 CT-TGGTCT
126 TTATAATTT
* * *
193547 CCTTTAGTTGGCTTTATCGA-TTTCACCTTAGTTAACACCCTTTTCAACTTAGGTTTCATCCTAG
1 CCTTTAGTTGGCTTTAT-GAGTTTCACCCTAGTCAACAACCTTTTCAACTTAGGTTTCATCCTAG
* *
193611 TCACCTTTAGTTGACTTCATTGGTTTT-ACCCTTG-TCA-ACCCTTTTCAACTTAGGTTCTGTTA
65 TCACCTTTAGTTGACTTCATTGGTTTTGA-CCTAGTTAACACCCTTTTCAACTTAGGTTCTGTTA
193673 TAATTT
129 TAATTT
* * * * **
193679 CCTTTAGTTGTCTTTATTAGTTTTACCCTAGTCAACAACTTTTTTGACTTAGGTTTCATCCTAGT
1 CCTTTAGTTGGCTTTATGAGTTTCACCCTAGTCAACAACCTTTTCAACTTAGGTTTCATCCTAGT
* * * *
193744 CACTTTTAGTTGACTTTATTTGTTTTGATCTAGTTAACACCCTTTTCAACTTAGGTT
66 CACCTTTAGTTGACTTCATTGGTTTTGACCTAGTTAACACCCTTTTCAACTTAGGTT
193801 TTTTCCTAGT
Statistics
Matches: 208, Mismatches: 35, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
131 18 0.09
132 117 0.56
133 46 0.22
134 27 0.13
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (134 bp):
CCTTTAGTTGGCTTTATGAGTTTCACCCTAGTCAACAACCTTTTCAACTTAGGTTTCATCCTAGT
CACCTTTAGTTGACTTCATTGGTTTTGACCTAGTTAACACCCTTTTCAACTTAGGTTCTGTTATA
ATTT
Found at i:193780 original size:199 final size:196
Alignment explanation
Indices: 193392--194066 Score: 591
Period size: 199 Copynumber: 3.4 Consensus size: 196
193382 TGGCCAACAC
* * *
193392 CAACTTAGGTTTCGTCCTAGTCACCTTTAGTTAACTTTATCGGTTTCACCCTAGTCAACTCTTTT
1 CAACTTAGGTTTCATCCTAGTCACCTTTAGTTAACTTTATCGGTTTTACCCTAGTCAAC-CCTTT
* * * * * *
193457 TCGACTTAGGTTTCACTCTAA-CCACTTTAAGTTGACTTTATTGGTTTCACCCTAGTTAACACCT
65 TCAACTTAGGTTT-GCT-TAATTC-CTTT-AGTTGTCTTTATTAGTTTCACCCTAGTCAACACCT
* * * * *
193521 TTTTTTACTTAGGTTTCA-CTTGGTCTCCTTTAGTTGGCTTTA-TCGATTTCACCTTAGTTAACA
126 TTTTTGACTTAGGTTTCATCCTAGTC-ACTTTAGTTGACTTTATTCGATTTCACCTTAGTTAACA
193584 CCCTTTT
190 CCCTTTT
* * * *
193591 CAACTTAGGTTTCATCCTAGTCACCTTTAGTTGACTTCATTGGTTTTACCCTTGTCAACCCTTTT
1 CAACTTAGGTTTCATCCTAGTCACCTTTAGTTAACTTTATCGGTTTTACCCTAGTCAACCCTTTT
* * *
193656 CAACTTAGGTTCTGTTATAATTTCCTTTAGTTGTCTTTATTAGTTTTACCCTAGTCAACAACTTT
66 CAACTTAGGTT-TGCT-TAA-TTCCTTTAGTTGTCTTTATTAGTTTCACCCTAGTCAACACCTTT
* * * *
193721 TTTGACTTAGGTTTCATCCTAGTCACTTTTAGTTGACTTTATTTGTTTTGATC-TAGTTAACACC
128 TTTGACTTAGGTTTCATCCTAGTCAC-TTTAGTTGACTTTATTCGATTTCACCTTAGTTAACACC
193785 CTTTT
192 CTTTT
** ** * * *
193790 CAACTTAGGTTTTTTCCTAGTCATTTTTAGTTAACTTTATCGATTTTGCCCTAGCCAACACCCTT
1 CAACTTAGGTTTCATCCTAGTCACCTTTAGTTAACTTTATCGGTTTTACCCTAGTC-A-ACCCTT
* ** * * *
193855 TTCAACTTAAGTTTTGCCTTGGTATCCTTTAGTT-TACTTTATCAGTTTCACCTTGGTCAACACC
64 TTCAACTT-AGGTTTG-CTTAAT-TCCTTTAGTTGT-CTTTATTAGTTTCACCCTAGTCAACACC
* * * *
193919 TTTTTTGACTTATGTATT-GTCCTAGTCAACTTTAGTTGATTTTA-TC-AGTTTCACATTAGTTA
125 TTTTTTGACTTAGGT-TTCATCCTAGTC-ACTTTAGTTGACTTTATTCGA-TTTCACCTTAGTTA
*
193981 ATTA---TTTT
187 A-CACCCTTTT
* * * * * ** *
193989 -TACTTAGGTTTCATCCTAGTCTCTTTTAGTTGATTTTATTTGTTTTGCCCTAGTCAATACCCTT
1 CAACTTAGGTTTCATCCTAGTCACCTTTAGTTAACTTTATCGGTTTTACCCTAGTC-A-ACCCTT
**
194053 TTTGACTTAGGTTT
64 TTCAACTTAGGTTT
194067 TATCCTAGTC
Statistics
Matches: 389, Mismatches: 70, Indels: 36
0.79 0.14 0.07
Matches are distributed among these distances:
197 5 0.01
198 125 0.32
199 141 0.36
200 16 0.04
201 92 0.24
202 10 0.03
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.47
Consensus pattern (196 bp):
CAACTTAGGTTTCATCCTAGTCACCTTTAGTTAACTTTATCGGTTTTACCCTAGTCAACCCTTTT
CAACTTAGGTTTGCTTAATTCCTTTAGTTGTCTTTATTAGTTTCACCCTAGTCAACACCTTTTTT
GACTTAGGTTTCATCCTAGTCACTTTAGTTGACTTTATTCGATTTCACCTTAGTTAACACCCTTT
T
Found at i:195957 original size:79 final size:80
Alignment explanation
Indices: 195848--196110 Score: 282
Period size: 78 Copynumber: 3.3 Consensus size: 80
195838 TGATCCTTGG
* *
195848 AAATAACGGGGTTAGAGTATCCCCGAGATGAAAAATTTAATA-ATTTGAAAATAAAAACGGAGTT
1 AAATAATGGGGTTGGAGTATCCCCGAGATGAAAAATTTAATATATTTGAAAATAAAAACGGAGTT
*
195912 GGAGTA-TCTCCTCAG
66 GGAGTATTC-CCTCAA
* * * * * * * * *
195927 AATTGATGGGGTTGGAGTATCCTCGTGATGAAAATTTTAATATTTTTGGAAATAAAAATGGGGTT
1 AAATAATGGGGTTGGAGTATCCCCGAGATGAAAAATTTAATATATTTGAAAATAAAAACGGAGTT
195992 GGAGTATTCCCTCAA
66 GGAGTATTCCCTCAA
** * * * *
196007 AAATAATGGGGTTGGAGTATCCCC-A-ATGGTAAATTTAACATCTTTGAAAATAAAAATGGGGTT
1 AAATAATGGGGTTGGAGTATCCCCGAGATGAAAAATTTAATATATTTGAAAATAAAAACGGAGTT
* *
196070 GAAGTATCCCCTCAA
66 GGAGTATTCCCTCAA
* * *
196085 AAATAACGAGGTTGGACTATCCCCGA
1 AAATAATGGGGTTGGAGTATCCCCGA
196111 AAAAAATCGA
Statistics
Matches: 154, Mismatches: 27, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
78 66 0.43
79 36 0.23
80 50 0.32
81 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (80 bp):
AAATAATGGGGTTGGAGTATCCCCGAGATGAAAAATTTAATATATTTGAAAATAAAAACGGAGTT
GGAGTATTCCCTCAA
Found at i:197734 original size:20 final size:20
Alignment explanation
Indices: 197709--197748 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
197699 ATTGTAAGCA
197709 TGTATCGATACATTTACTTG
1 TGTATCGATACATTTACTTG
*
197729 TGTATCGATACATTTCCTTG
1 TGTATCGATACATTTACTTG
197749 GCAGTATGCA
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:0.17, G:0.15, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTACTTG
Found at i:198187 original size:39 final size:40
Alignment explanation
Indices: 198114--198194 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 40
198104 TGTTTACAAG
198114 TTTCACCCCGGTTAACCTTTTTTTTTTTACTTAAGTTTTAT
1 TTTCACCCCGGTTAACC-TTTTTTTTTTACTTAAGTTTTAT
198155 TTTCACCCCGGTTAACC-TTTTTTTTTACTTAAGTTTTAT
1 TTTCACCCCGGTTAACCTTTTTTTTTTACTTAAGTTTTAT
198194 T
1 T
198195 CTAGTCACTC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 23 0.57
41 17 0.43
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.56
Consensus pattern (40 bp):
TTTCACCCCGGTTAACCTTTTTTTTTTACTTAAGTTTTAT
Found at i:199847 original size:13 final size:13
Alignment explanation
Indices: 199829--199854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
199819 CAATTTTTTG
199829 TGTATCGATACAT
1 TGTATCGATACAT
199842 TGTATCGATACAT
1 TGTATCGATACAT
199855 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:199919 original size:21 final size:21
Alignment explanation
Indices: 199893--199968 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
199883 CTGCCAAGAA
199893 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
199914 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
199934 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
199955 ATGTATCGATACAT
1 ATGTATCGATACAT
199969 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:199938 original size:20 final size:20
Alignment explanation
Indices: 199913--199986 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
199903 ACATCTTTTT
199913 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
199933 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
199954 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
199974 CATGTATCGATAC
1 CATGTATCGATAC
199987 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:199950 original size:41 final size:41
Alignment explanation
Indices: 199893--199986 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
199883 CTGCCAAGAA
199893 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
199934 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
199975 ATGTATCGATAC
1 ATGTATCGATAC
199987 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:202456 original size:13 final size:13
Alignment explanation
Indices: 202438--202475 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
202428 ATAATCACCC
202438 TGTATCGATACAG
1 TGTATCGATACAG
*
202451 TGTATCGATACAT
1 TGTATCGATACAG
202464 TGTATCGATACA
1 TGTATCGATACA
202476 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:202489 original size:20 final size:20
Alignment explanation
Indices: 202464--202540 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
202454 ATCGATACAT
202464 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
202484 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
*
202509 TGTATCGATACACAA-AAACA
1 TGTATCGATACA-AAGAAAAA
202529 TGTATCGATACA
1 TGTATCGATACA
202541 TTTTGGACAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 30 0.64
25 16 0.34
26 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:202693 original size:8 final size:8
Alignment explanation
Indices: 202680--202711 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
202670 CATCATTCAA
202680 CACAAAAT
1 CACAAAAT
202688 CACAAAAT
1 CACAAAAT
202696 CACAAAAT
1 CACAAAAT
202704 CACAAAAT
1 CACAAAAT
202712 TTAATCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.62, C:0.25, G:0.00, T:0.12
Consensus pattern (8 bp):
CACAAAAT
Found at i:206428 original size:21 final size:21
Alignment explanation
Indices: 206399--206443 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
206389 AAGTTTTCAT
*
206399 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
206419 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
206441 TTT
1 TTT
206444 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:208670 original size:13 final size:13
Alignment explanation
Indices: 208652--208677 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
208642 CAATTTTTTG
208652 TGTATCGATACAT
1 TGTATCGATACAT
208665 TGTATCGATACAT
1 TGTATCGATACAT
208678 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:218563 original size:20 final size:20
Alignment explanation
Indices: 218534--218602 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
218524 GTAAAAAGAT
*
218534 AGAATATATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
218554 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
218574 TA-CATGTATCGATACGTTGA
1 -AGAATGTATCGATACATTGA
*
218594 AAAATGTAT
1 AGAATGTAT
218603 TAATACATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.02
20 39 0.95
21 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:219684 original size:29 final size:29
Alignment explanation
Indices: 219539--219967 Score: 437
Period size: 28 Copynumber: 14.8 Consensus size: 29
219529 GGCTTTTAGA
*
219539 AAAAGG-TGCCACTAACTTGTGTGGGCTTTG
1 AAAAGGATGCCACTGAC-T-TGTGGGCTTTG
* *
219569 AAAAGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAG-GATGCCACTGAC-T-TGTGGGCTTTG
* *
219601 AAAAGAGTTACCACTGACTTGTGGGCTTTG
1 AAAAG-GATGCCACTGACTTGTGGGCTTTG
* **
219631 AAAAGAGTTATCACT-AGCTTGTGGGCTTTG
1 AAAAG-GATGCCACTGA-CTTGTGGGCTTTG
*
219661 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
219690 AAAATG-TGCCATTAACTTGTGAGCTTTG
1 AAAAGGATGCCACTGACTTGTGGGCTTTG
* *
219718 AAATGG-TGCCACTGACTTGTGGGCATTG
1 AAAAGGATGCCACTGACTTGTGGGCTTTG
*
219746 -AAAGGATGGCACTGACTTGTGGGCTTTG
1 AAAAGGATGCCACTGACTTGTGGGCTTTG
* *
219774 -AAAGGATGGCACTAACTTGTGGGCTTTG
1 AAAAGGATGCCACTGACTTGTGGGCTTTG
*
219802 AAAA-GATGCCACTAACTTGTGGGCTTTG
1 AAAAGGATGCCACTGACTTGTGGGCTTTG
*
219830 AGAAGGATGCCA-TCGACTTGTGGGCTTTG
1 AAAAGGATGCCACT-GACTTGTGGGCTTTG
*
219859 AGAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
219888 AGAAGGATACCGCTGACTTATGGGCTTT-
1 AAAAGGATGCCACTGACTTGTGGGCTTTG
* **
219916 AAAAGGATGCCACTAACTTGTGGTTTTTTG
1 AAAAGGATGCCACTGACTTGTGG-GCTTTG
*
219946 AAGA-GATGCCACTGACTTGTGG
1 AAAAGGATGCCACTGACTTGTGG
219968 TTTTTTGAAG
Statistics
Matches: 351, Mismatches: 37, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.01
28 133 0.38
29 121 0.34
30 53 0.15
31 2 0.01
32 38 0.11
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (29 bp):
AAAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:224962 original size:13 final size:13
Alignment explanation
Indices: 224944--224968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
224934 ATATTGCACA
224944 GTATCGATACATT
1 GTATCGATACATT
224957 GTATCGATACAT
1 GTATCGATACAT
224969 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:225093 original size:20 final size:20
Alignment explanation
Indices: 225050--225101 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
225040 CTTAAATGTT
*
225050 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
225069 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
225089 TGTATCGATACAT
1 TGTATCGATACAT
225102 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:226153 original size:13 final size:13
Alignment explanation
Indices: 226135--226159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
226125 ATGTTGCACA
226135 GTATCGATACATT
1 GTATCGATACATT
226148 GTATCGATACAT
1 GTATCGATACAT
226160 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:226172 original size:20 final size:21
Alignment explanation
Indices: 226147--226199 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
226137 ATCGATACAT
**
226147 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
226167 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
226188 TGTATCGATACA
1 TGTATCGATACA
226200 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:226269 original size:13 final size:13
Alignment explanation
Indices: 226251--226275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
226241 GCACACAGTA
226251 TGTATCGATACAT
1 TGTATCGATACAT
226264 TGTATCGATACA
1 TGTATCGATACA
226276 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.