Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1092
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: 788722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:721767 original size:33 final size:33
Alignment explanation
Indices: 721710--721775 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
721700 GCCAAGGAAA
*
721710 TGTATCGATACATTATTCAATGTATTGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
**
721743 TGTATCGATACATTGA-TCTTTGTATCGATACAT
1 TGTATCGATACATT-ATTCAATGTATCGATACAT
721776 CTGGAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTATTCAATGTATCGATACAT
Found at i:722586 original size:13 final size:13
Alignment explanation
Indices: 722568--722593 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
722558 CAATTTTTTG
722568 TGTATCGATACAT
1 TGTATCGATACAT
722581 TGTATCGATACAT
1 TGTATCGATACAT
722594 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:723314 original size:21 final size:21
Alignment explanation
Indices: 723288--723349 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
723278 CTCTCCTTTG
* *
723288 TCTCCCCCGTTTATTAA-TAAA
1 TCTCCCCC-TTAATCAAGTAAA
723309 TCTCCCCCTTAATCAAGTAAA
1 TCTCCCCCTTAATCAAGTAAA
723330 TCTCCCCCTTAATCAAGTAA
1 TCTCCCCCTTAATCAAGTAA
723350 TTCTGTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.31, C:0.32, G:0.05, T:0.32
Consensus pattern (21 bp):
TCTCCCCCTTAATCAAGTAAA
Found at i:723364 original size:29 final size:29
Alignment explanation
Indices: 723325--723381 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
723315 CCTTAATCAA
723325 GTAAATCTCCCCCTTAATCAAGTAATTCT
1 GTAAATCTCCCCCTTAATCAAGTAATTCT
*
723354 GTAAATTTCCCCCTTAATCAAGTAATTC
1 GTAAATCTCCCCCTTAATCAAGTAATTC
723382 ATATCAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (29 bp):
GTAAATCTCCCCCTTAATCAAGTAATTCT
Found at i:725192 original size:13 final size:13
Alignment explanation
Indices: 725174--725212 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
725164 ATAATCACCC
*
725174 TGTATCGATACAG
1 TGTATCGATACAA
725187 TGTATCGATACAA
1 TGTATCGATACAA
725200 TGTATCGATACAA
1 TGTATCGATACAA
725213 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:725223 original size:20 final size:20
Alignment explanation
Indices: 725198--725276 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
725188 GTATCGATAC
725198 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
* *
725218 AATGTATCAATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
725243 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
725263 CATGTATCGATACA
1 AATGTATCGATACA
725277 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
25 17 0.35
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:727311 original size:15 final size:15
Alignment explanation
Indices: 727291--727321 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
727281 ATTTCGTTTG
*
727291 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
727306 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
727321 G
1 G
727322 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:729154 original size:21 final size:21
Alignment explanation
Indices: 729125--729169 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
729115 AAGTTTTCAT
*
729125 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
729145 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
729167 TTT
1 TTT
729170 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:731414 original size:13 final size:13
Alignment explanation
Indices: 731396--731421 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
731386 CAATTTTTTG
731396 TGTATCGATACAT
1 TGTATCGATACAT
731409 TGTATCGATACAT
1 TGTATCGATACAT
731422 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:734131 original size:19 final size:19
Alignment explanation
Indices: 734107--734165 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
734097 AGCAAATATG
734107 TCGATACATAAGTGTTGTA
1 TCGATACATAAGTGTTGTA
734126 TCGATAC--AA----TGTA
1 TCGATACATAAGTGTTGTA
734139 TCGATACATAAGTGTTGTA
1 TCGATACATAAGTGTTGTA
734158 TCGATACA
1 TCGATACA
734166 ATGTATCGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.32
15 2 0.06
17 2 0.06
19 19 0.56
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (19 bp):
TCGATACATAAGTGTTGTA
Found at i:734140 original size:13 final size:13
Alignment explanation
Indices: 734122--734179 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
734112 ACATAAGTGT
734122 TGTATCGATACAA
1 TGTATCGATACAA
734135 TGTATCGATACATAA
1 TGTATCGATAC--AA
734150 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
734167 TGTATCGCTACAA
1 TGTATCGATACAA
734180 AGCTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:734148 original size:32 final size:32
Alignment explanation
Indices: 734107--734178 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
734097 AGCAAATATG
734107 TCGATACATAAGTGTTGTATCGATACAATGTA
1 TCGATACATAAGTGTTGTATCGATACAATGTA
734139 TCGATACATAAGTGTTGTATCGATACAATGTA
1 TCGATACATAAGTGTTGTATCGATACAATGTA
*
734171 TCGCTACA
1 TCGATACA
734179 AAGCTACTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (32 bp):
TCGATACATAAGTGTTGTATCGATACAATGTA
Found at i:734254 original size:33 final size:33
Alignment explanation
Indices: 734197--734262 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
734187 GCCAAGGAAA
*
734197 TGTATCGATACATTATTCAATGTATTGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
**
734230 TGTATCGATACATTGA-TCTTTGTATCGATACAT
1 TGTATCGATACATT-ATTCAATGTATCGATACAT
734263 CTGGAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTATTCAATGTATCGATACAT
Found at i:735073 original size:13 final size:13
Alignment explanation
Indices: 735055--735080 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
735045 CAATTTTTTG
735055 TGTATCGATACAT
1 TGTATCGATACAT
735068 TGTATCGATACAT
1 TGTATCGATACAT
735081 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:739811 original size:21 final size:20
Alignment explanation
Indices: 739787--739833 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
739777 CTATAATTTT
*
739787 TATCGATACAACAAGTTAATG
1 TATCGATAC-ACAAGTGAATG
* *
739808 TATCAATACATAAGTGAATG
1 TATCGATACACAAGTGAATG
739828 TATCGA
1 TATCGA
739834 CACATGCTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
TATCGATACACAAGTGAATG
Found at i:739838 original size:20 final size:20
Alignment explanation
Indices: 739799--739838 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
739789 TCGATACAAC
* *
739799 AAGTTAATGTATCAATACAT
1 AAGTGAATGTATCAACACAT
*
739819 AAGTGAATGTATCGACACAT
1 AAGTGAATGTATCAACACAT
739839 GCTTGAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (20 bp):
AAGTGAATGTATCAACACAT
Found at i:739923 original size:21 final size:21
Alignment explanation
Indices: 739897--739951 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
739887 TTGGAAAAAT
*
739897 TGTATCGATACATGCTTATAA
1 TGTATCGATACATGCTTACAA
*
739918 TGTATCGATACATGCTTGCAA
1 TGTATCGATACATGCTTACAA
739939 TGTATCGATACAT
1 TGTATCGATACAT
739952 TTTTCAGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATGCTTACAA
Found at i:740448 original size:14 final size:14
Alignment explanation
Indices: 740429--740459 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
740419 GCTAAGGACT
740429 TTTTTTTAGCCACA
1 TTTTTTTAGCCACA
740443 TTTTTTTAGCCACA
1 TTTTTTTAGCCACA
740457 TTT
1 TTT
740460 CCAGCCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTTTTTAGCCACA
Found at i:740940 original size:20 final size:21
Alignment explanation
Indices: 740915--740953 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
740905 ATCTTAATAG
740915 GCCATGTT-CATGCATTTTGT
1 GCCATGTTCCATGCATTTTGT
740935 GCCATGTTCCATGCATTTT
1 GCCATGTTCCATGCATTTT
740954 AACATGCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (21 bp):
GCCATGTTCCATGCATTTTGT
Found at i:744194 original size:25 final size:24
Alignment explanation
Indices: 744153--744216 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 24
744143 GGTTGCTGCT
*
744153 AAAAAAGAGAGAAAAAAAGAAAGAA
1 AAAAAAAAGA-AAAAAAAGAAAGAA
*
744178 AAAAAAAAGAAAGAAAAAGAGAGAA
1 AAAAAAAAGAAA-AAAAAGAAAGAA
744203 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
744217 CTAGGAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 4 0.11
25 32 0.89
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAAGAAAGAA
Found at i:744196 original size:21 final size:21
Alignment explanation
Indices: 744164--744216 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
744154 AAAAAGAGAG
744164 AAAAAAAG--AAAGA-AAAAA
1 AAAAAAAGAAAAAGAGAAAAA
*
744182 AAAAGAAAGAAAAAGAGAGAAA
1 AAAA-AAAGAAAAAGAGAAAAA
744204 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
744217 CTAGGAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.13
19 4 0.13
21 14 0.47
22 8 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAAGAAAAAGAGAAAAA
Found at i:744212 original size:15 final size:15
Alignment explanation
Indices: 744164--744195 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
744154 AAAAAGAGAG
744164 AAAAAAAGAAAGAAA
1 AAAAAAAGAAAGAAA
744179 AAAAAAAGAAAGAAA
1 AAAAAAAGAAAGAAA
744194 AA
1 AA
744196 GAGAGAAAAA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAGAAA
Found at i:747828 original size:29 final size:29
Alignment explanation
Indices: 747735--747828 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
747725 GGATTCATTT
747735 TTATATACAAAATTCATGCATCAAAAGGGA
1 TTATATACAAAATTCATGCATC-AAAGGGA
* * * ***
747765 TTAAAT-CGAAATAAT-ATTGAATCAAA-TTT
1 TTATATAC-AAA-ATTCA-TGCATCAAAGGGA
747794 TTATATACAAAATTCATGCATCAAAGGGA
1 TTATATACAAAATTCATGCATCAAAGGGA
747823 TTATAT
1 TTATAT
747829 TGAAATAAGG
Statistics
Matches: 46, Mismatches: 12, Indels: 13
0.65 0.17 0.18
Matches are distributed among these distances:
28 10 0.22
29 16 0.35
30 13 0.28
31 7 0.15
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (29 bp):
TTATATACAAAATTCATGCATCAAAGGGA
Found at i:749001 original size:13 final size:13
Alignment explanation
Indices: 748983--749008 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
748973 ACATACAAGA
748983 TGTATCGATACAT
1 TGTATCGATACAT
748996 TGTATCGATACAT
1 TGTATCGATACAT
749009 GACCAAATGT
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:749003 original size:32 final size:33
Alignment explanation
Indices: 748963--749030 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
748953 CCTTAATTGT
748963 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1 TTGTATCGATACATGACCAA-ATGTATCGATACA
*
748995 TTGTATCGATACATGACCAAATGTATTGATACA
1 TTGTATCGATACATGACCAAATGTATCGATACA
749028 TTG
1 TTG
749031 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCGATACA
Found at i:755195 original size:13 final size:13
Alignment explanation
Indices: 755177--755202 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
755167 CAGCATTCTC
755177 TGTATCGATACAA
1 TGTATCGATACAA
755190 TGTATCGATACAA
1 TGTATCGATACAA
755203 AGGGTTTATA
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:758174 original size:13 final size:13
Alignment explanation
Indices: 758156--758181 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
758146 CAATTTTTTG
758156 TGTATCGATACAT
1 TGTATCGATACAT
758169 TGTATCGATACAT
1 TGTATCGATACAT
758182 ACTTTGTGTA
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:758193 original size:32 final size:33
Alignment explanation
Indices: 758136--758199 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
758126 TACAAGCCAA
**
758136 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
758169 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
758200 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:758863 original size:18 final size:18
Alignment explanation
Indices: 758840--758875 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
758830 AATCAAAATA
758840 ATTTTAACAAATTCGTAC
1 ATTTTAACAAATTCGTAC
758858 ATTTTAACAAATTCGTAC
1 ATTTTAACAAATTCGTAC
758876 TTTCTCCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (18 bp):
ATTTTAACAAATTCGTAC
Found at i:758964 original size:21 final size:20
Alignment explanation
Indices: 758913--758961 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
758903 GTATTCGTAC
758913 ATTCTCCCCTTTTATTAACA
1 ATTCTCCCCTTTTATTAACA
758933 ATTCTCCCCTTTTATTAACA
1 ATTCTCCCCTTTTATTAACA
758953 ATTCTCCCC
1 ATTCTCCCC
758962 CTTAATCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.35, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTCTCCCCTTTTATTAACA
Found at i:760793 original size:13 final size:13
Alignment explanation
Indices: 760774--760812 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
760764 TATAATCCCT
*
760774 CTGTATCGATATA
1 CTGTATCGATACA
*
760787 GTGTATCGATACA
1 CTGTATCGATACA
760800 CTGTATCGATACA
1 CTGTATCGATACA
760813 AAGAAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:762913 original size:15 final size:15
Alignment explanation
Indices: 762893--762923 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
762883 ATTTCGTTTG
*
762893 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
762908 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
762923 G
1 G
762924 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:767011 original size:13 final size:13
Alignment explanation
Indices: 766993--767018 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
766983 CAATTTTTTG
766993 TGTATCGATACAT
1 TGTATCGATACAT
767006 TGTATCGATACAT
1 TGTATCGATACAT
767019 ACTTTGTGTA
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:767030 original size:32 final size:33
Alignment explanation
Indices: 766973--767036 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
766963 TACAAGCCAA
**
766973 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
767006 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
767037 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:767740 original size:13 final size:13
Alignment explanation
Indices: 767722--767746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
767712 ATAATGCACA
767722 GTATCGATACATT
1 GTATCGATACATT
767735 GTATCGATACAT
1 GTATCGATACAT
767747 GACCACTGCA
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:767853 original size:13 final size:13
Alignment explanation
Indices: 767835--767860 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
767825 ACATACAAGA
767835 TGTATCGATACAT
1 TGTATCGATACAT
767848 TGTATCGATACAT
1 TGTATCGATACAT
767861 GAGCAAATGT
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:767876 original size:33 final size:32
Alignment explanation
Indices: 767815--767882 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
767805 CCTTAACTGT
767815 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
767847 TTGTATCGATACATGAGCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
767880 TTG
1 TTG
767883 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 17 0.50
34 3 0.09
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:773018 original size:52 final size:52
Alignment explanation
Indices: 772873--772998 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
772863 AATATGAAAT
*
772873 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGCAAA
*
772925 TTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGCAAA
*
772977 TTTGTCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
772999 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGCAAA
Found at i:773025 original size:13 final size:13
Alignment explanation
Indices: 773007--773031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
772997 CAAAGATCAG
773007 TGTATCGATACAA
1 TGTATCGATACAA
773020 TGTATCGATACA
1 TGTATCGATACA
773032 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:774231 original size:20 final size:21
Alignment explanation
Indices: 774206--774244 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
774196 TTCCCGTGTA
774206 AATGTATCGATACA-ATTTTT
1 AATGTATCGATACATATTTTT
774226 AATGTATCGATACATATTT
1 AATGTATCGATACATATTT
774245 GAAAATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
AATGTATCGATACATATTTTT
Found at i:774317 original size:13 final size:13
Alignment explanation
Indices: 774299--774324 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
774289 CAATTTTTGG
774299 TGTATCGATACAT
1 TGTATCGATACAT
774312 TGTATCGATACAT
1 TGTATCGATACAT
774325 ACTTGGTGTA
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:774336 original size:32 final size:33
Alignment explanation
Indices: 774279--774342 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
774269 TACAAGCCAA
**
774279 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
774312 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
774343 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:774349 original size:19 final size:18
Alignment explanation
Indices: 774279--774349 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
774269 TACAAGCCAA
774279 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
774299 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
774312 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
774331 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
774350 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:778988 original size:15 final size:15
Alignment explanation
Indices: 778968--778998 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
778958 ATTTCGTTTG
*
778968 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
778983 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
778998 G
1 G
778999 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:780830 original size:21 final size:21
Alignment explanation
Indices: 780801--780845 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
780791 AAGTTTTTAT
*
780801 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
780821 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
780843 TTT
1 TTT
780846 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:783605 original size:13 final size:13
Alignment explanation
Indices: 783587--783615 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
783577 ACAATGTTCT
783587 TTGTATCGATACA
1 TTGTATCGATACA
783600 TTGTATCGATACA
1 TTGTATCGATACA
783613 TTG
1 TTG
783616 GTTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:785441 original size:77 final size:77
Alignment explanation
Indices: 785314--785504 Score: 346
Period size: 77 Copynumber: 2.5 Consensus size: 77
785304 AAAGGGGGAG
*
785314 AAATGTTTGAAAATAAATTTATATCAAGGGGGAGAAATTTTTTAAAACAAAAGCCTTAATTATTT
1 AAATGTTTGAAAATAAATTTTTATCAAGGGGGAGAAATTTTTTAAAACAAAAGCCTTAATTATTT
*
785379 TATCGAGGAATT
66 TATCAAGGAATT
785391 AAATGTTTGAAAATAAATTTTTATCAAGGGGGAGAAATTTTTTAAAACAAAAGCCTTAATTATTT
1 AAATGTTTGAAAATAAATTTTTATCAAGGGGGAGAAATTTTTTAAAACAAAAGCCTTAATTATTT
785456 TATCAAGGAATT
66 TATCAAGGAATT
* *
785468 AAATGTTTGAAAATAATTTTTTATTAAGGGGGAGAAA
1 AAATGTTTGAAAATAAATTTTTATCAAGGGGGAGAAA
785505 AATGAAACTT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 110 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (77 bp):
AAATGTTTGAAAATAAATTTTTATCAAGGGGGAGAAATTTTTTAAAACAAAAGCCTTAATTATTT
TATCAAGGAATT
Found at i:786056 original size:13 final size:13
Alignment explanation
Indices: 786038--786064 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
786028 ATATTATGCT
786038 TTGTATCGATACA
1 TTGTATCGATACA
786051 TTGTATCGATACA
1 TTGTATCGATACA
786064 T
1 T
786065 GTTCATTGCC
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):
TTGTATCGATACA
Found at i:786189 original size:33 final size:33
Alignment explanation
Indices: 786134--786196 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
786124 TACCACTGTT
* *
786134 TGTATCGATACATGGCACATTGTATCGATGTAA
1 TGTATCGATACATGACAAATTGTATCGATGTAA
* *
786167 TGTATCGATACATGATAAATTGTATTGATG
1 TGTATCGATACATGACAAATTGTATCGATG
786197 CATTGCTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATGACAAATTGTATCGATGTAA
Done.