Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1214
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: 92295
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:7878 original size:15 final size:14
Alignment explanation
Indices: 7860--7897 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
7850 TATTATGCCT
7860 TAAAAAAACAAAAAA
1 TAAAAAAA-AAAAAA
7875 TAAAAAATAAAAAAA
1 TAAAAAA-AAAAAAA
7890 TAAAAAAA
1 TAAAAAAA
7898 TTGAATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.11
Consensus pattern (14 bp):
TAAAAAAAAAAAAA
Found at i:7879 original size:6 final size:7
Alignment explanation
Indices: 7862--7896 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
7852 TTATGCCTTA
*
7862 AAAAAAC
1 AAAAAAT
7869 AAAAAAT
1 AAAAAAT
7876 AAAAAAT
1 AAAAAAT
7883 AAAAAAAT
1 -AAAAAAT
7891 AAAAAA
1 AAAAAA
7897 ATTGAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.89, C:0.03, G:0.00, T:0.09
Consensus pattern (7 bp):
AAAAAAT
Found at i:7881 original size:9 final size:8
Alignment explanation
Indices: 7860--7898 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
7850 TATTATGCCT
7860 TAAAAAAA
1 TAAAAAAA
*
7868 -CAAAAAA
1 TAAAAAAA
7875 T-AAAAAA
1 TAAAAAAA
7882 TAAAAAAA
1 TAAAAAAA
7890 TAAAAAAA
1 TAAAAAAA
7898 T
1 T
7899 TGAATGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 13 0.46
8 15 0.54
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (8 bp):
TAAAAAAA
Found at i:9247 original size:132 final size:130
Alignment explanation
Indices: 8952--9447 Score: 514
Period size: 132 Copynumber: 3.7 Consensus size: 130
8942 CCACTTTGCC
* *
8952 TAGTCAAGTTTCTTTTCCTTTCTG-TTTGACATATGGTTACCACCCTTGGTCAAACTCT-TCTCA
1 TAGTCAA-TTT-TTTT-CATTCTGATTTGAC-TATGGTTACCACCC-TGGTCAAA-TCTGCCTC-
* ** * * * *
9015 ATTCATGTCTGATGTATGGTTACCACCCTGGTCAAACTCTTCTCAATTCATGTCTGATGTATGGT
59 TTTTTTGTTTGATGTATGGTTACCACCCTGGTCAAACTCTTCTC-ATTTAGGTTTGATGTATGGT
*
9080 TACCACCC
123 TACCACCT
* * * *
9088 TAGTTAAATTTCTTTCATTCTGATTTGACGTATGGTTACCACCTTAGTCAAATCTGCCTCTTTTT
1 TAG-TCAATTTTTTTCATTCTGATTTGAC-TATGGTTACCACCCTGGTCAAATCTGCCTCTTTTT
* * *
9153 TGTTTGATGTATAGTTATCACCCTGGTCAAACTCTTCTCATTTGGGTTTGATGTATGGTTACCAC
64 TGTTTGATGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTAGGTTTGATGTATGGTTACCAC
9218 CT
129 CT
* *
9220 TAGTCAATTTTTTTTCATTATGTTTTGACATATGGTTACCACCCTGGTCAAATCTGCCTCTTTTT
1 TAGTCAA-TTTTTTTCATTCTGATTTGAC-TATGGTTACCACCCTGGTCAAATCTGCCTCTTTTT
* ** * * ** *
9285 TATTTGACATATGGTTACCACCCTAGTTAAACTCTT-TCCATTTAGGTTTGACATATAGTTACCA
64 TGTTTGATGTATGGTTACCACCCTGGTCAAACTCTTCT-CATTTAGGTTTGATGTATGGTTACCA
9349 CCT
128 CCT
* * * * ** **
9352 TGGTCAGATTCTTTTCATTCTAATTTGACTATGGTTACTACCCTGGTCAAAT-TCGCCTCCATCC
1 TAGTCA-ATTTTTTTCATTCTGATTTGACTATGGTTACCACCCTGGTCAAATCT-GCCTCTTTTT
9416 TGTTTGATGTATGGTTACCACCCTGGTCAAAC
64 TGTTTGATGTATGGTTACCACCCTGGTCAAAC
9448 GATTTGCATT
Statistics
Matches: 302, Mismatches: 51, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
130 1 0.00
131 59 0.20
132 153 0.51
133 42 0.14
134 16 0.05
135 22 0.07
136 6 0.02
137 3 0.01
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (130 bp):
TAGTCAATTTTTTTCATTCTGATTTGACTATGGTTACCACCCTGGTCAAATCTGCCTCTTTTTTG
TTTGATGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTAGGTTTGATGTATGGTTACCACCT
Found at i:9464 original size:44 final size:43
Alignment explanation
Indices: 8974--9470 Score: 290
Period size: 44 Copynumber: 11.3 Consensus size: 43
8964 TTTTCCTTTC
** *
8974 TGTTTGACATATGGTTACCACCCTTGGTCAAACTCTTCTCAATTCA
1 TGTTTGATGTATGGTTACCACCC-TGGTCAAACTCTT-TC-ATTCT
* *
9020 TGTCTGATGTATGGTTACCACCCTGGTCAAACTCTTCTCAATTCA
1 TGTTTGATGTATGGTTACCACCCTGGTCAAACTCTT-TC-ATTCT
* * * *
9065 TGTCTGATGTATGGTTACCACCCTAGTTAAATTTCTTTCATTC-
1 TGTTTGATGTATGGTTACCACCCTGGTCAAA-CTCTTTCATTCT
* * * * * *
9108 TGATTTGACGTATGGTTACCACCTTAGTCAAA-TCTGCCTCTTTTT
1 TG-TTTGATGTATGGTTACCACCCTGGTCAAACTCT--TTCATTCT
* *
9153 TGTTTGATGTATAGTTATCACCCTGGTCAAACTCTTCTCATT-T
1 TGTTTGATGTATGGTTACCACCCTGGTCAAACTCTT-TCATTCT
* * * ** * *
9196 GGGTTTGATGTATGGTTACCACCTTAGTCAATTTTTTTTCATT-A
1 -TGTTTGATGTATGGTTACCACCCTGGTCAA-ACTCTTTCATTCT
** * * *
9240 TGTTTTGACATATGGTTACCACCCTGGTCAAA-TCTGCCTCTTTTT
1 TG-TTTGATGTATGGTTACCACCCTGGTCAAACTCT--TTCATTCT
* ** * *
9285 TATTTGACATATGGTTACCACCCTAGTTAAACTCTTTCCATT-T
1 TGTTTGATGTATGGTTACCACCCTGGTCAAACTCTTT-CATTCT
* ** * * * *
9328 AGGTTTGACATATAGTTACCACCTTGGTCAGATTCTTTTCATTCT
1 -TGTTTGATGTATGGTTACCACCCTGGTCAAACTC-TTTCATTCT
** * * * * * *
9373 AATTTGA-CTATGGTTACTACCCTGGTCAAATTCGCCTCCA-TCC
1 TGTTTGATGTATGGTTACCACCCTGGTCAAA--CTCTTTCATTCT
**
9416 TGTTTGATGTATGGTTACCACCCTGGTCAAACGATTTGCATTCT
1 TGTTTGATGTATGGTTACCACCCTGGTCAAACTCTTT-CATTCT
9460 TGTTTGATGTA
1 TGTTTGATGTA
9471 ATTCAGACTT
Statistics
Matches: 356, Mismatches: 72, Indels: 48
0.75 0.15 0.10
Matches are distributed among these distances:
42 8 0.02
43 33 0.09
44 221 0.62
45 70 0.20
46 24 0.07
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (43 bp):
TGTTTGATGTATGGTTACCACCCTGGTCAAACTCTTTCATTCT
Found at i:12211 original size:25 final size:22
Alignment explanation
Indices: 12191--12233 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12181 TACATTAAGT
12191 ATTT-TTACTTTGAAAAACATTA
1 ATTTATTAC-TTGAAAAACATTA
*
12213 ATTTATTGCTTGAAAAACATT
1 ATTTATTACTTGAAAAACATT
12234 TAGACTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTTATTACTTGAAAAACATTA
Found at i:16165 original size:17 final size:18
Alignment explanation
Indices: 16128--16168 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
16118 CAGTAAATGC
*
16128 ATCGATACATAAGTTTTGT
1 ATCGAAACATAAG-TTTGT
16147 ATCGAAACATAAG-TTGT
1 ATCGAAACATAAGTTTGT
16164 ATCGA
1 ATCGA
16169 TACAATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
19 12 0.57
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (18 bp):
ATCGAAACATAAGTTTGT
Found at i:16223 original size:21 final size:21
Alignment explanation
Indices: 16197--16237 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
16187 GGCTACTACC
16197 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
16218 AAGGAAATGTATCGATACAT
1 AAGGAAATGTATCGATACAT
16238 CAATCTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:16784 original size:17 final size:17
Alignment explanation
Indices: 16762--16798 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
16752 ACCTTAGGGA
16762 ATTGGTTTTCAAACTCC
1 ATTGGTTTTCAAACTCC
16779 ATTGGTTTTCAAACTCC
1 ATTGGTTTTCAAACTCC
16796 ATT
1 ATT
16799 CCTGTAGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (17 bp):
ATTGGTTTTCAAACTCC
Found at i:18654 original size:53 final size:50
Alignment explanation
Indices: 18537--18657 Score: 170
Period size: 51 Copynumber: 2.3 Consensus size: 50
18527 CTTAGTTCTC
* *
18537 CACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACCAATTTT
1 CACAATCGAGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTT
* *
18587 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTT
1 C-ACAATCGAGGATACTCCAACTCCGATTTTATTTCC--AAAACACCAA-TTTT
18641 CACAATCGAGGATACTC
1 CACAATCGAGGATACTC
18658 TAACCCCGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
50 1 0.02
51 31 0.51
53 24 0.39
54 5 0.08
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (50 bp):
CACAATCGAGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTT
Found at i:18817 original size:79 final size:79
Alignment explanation
Indices: 18672--18988 Score: 372
Period size: 79 Copynumber: 4.0 Consensus size: 79
18662 CCCGTTAATC
* * * * *
18672 ATCGAGGATACTCCAACCCCGTTATTTTCGAGGGAGATACTGCAACCCCAGCTTTA-TTCTTAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGG-GATACTCCAACCCCGGCTTTATTTC-CAAA
*
18736 ATATTGATTTCTCATA
64 ATATTAATTTCTCATA
*
18752 ATCGGGGATACTCCAACTCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
18817 ATTAATTTCTCATA
66 ATTAATTTCTCATA
* * * *
18831 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCTGGTTTTATTT-CTAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
** * *
18895 CATCGATTTTTCACA
66 -ATTAATTTCTCATA
* * * * *
18910 ATCGGGGATACTCCAACCCAGTTATTTTCAAGGAGATACTCCAACCCC-G-TTACTATCTCCAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTT--TATTTCCAAA
18973 ATATTAAATTTCTCAT
64 ATATT-AATTTCTCAT
18989 CGGGAAATAT
Statistics
Matches: 203, Mismatches: 28, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
77 2 0.01
78 6 0.03
79 149 0.73
80 46 0.23
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
ATTAATTTCTCATA
Found at i:18913 original size:158 final size:159
Alignment explanation
Indices: 18672--18988 Score: 412
Period size: 158 Copynumber: 2.0 Consensus size: 159
18662 CCCGTTAATC
* * *
18672 ATCGAGGATACTCCAACCCCGTTATTTTCGAGGGAGATACTGCAACCCCAGCTTTATTCTTAAAA
1 ATCGAGGATACTCCAACCCCGTTATCTCCGAGGGAGATACTCCAACCCCAGCTTTATTCTTAAAA
* * * *
18737 TATTGATTTCTCATAATCGGGGATACTCCAACTCC-GTTATTTCCGAGGGGATACTCCAACCCCG
66 TATCGATTTCTCACAATCGGGGATACTCCAAC-CCAGTTATTTCCAAGGAGATACTCCAACCCC-
*
18801 GCTT-TATTTCCAAAATATT-AATTTCTCATA
129 G-TTATATCTCCAAAATATTAAATTTCTCATA
* ** *
18831 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGG-GATACTCCAACCCTGGTTTTATT-TCT-AA
1 ATCGAGGATACTCCAACCCCGTTATCTCCGAGGGAGATACTCCAACCCCAGCTTTATTCT-TAAA
* *
18893 ATCATCGATTTTTCACAATCGGGGATACTCCAACCCAGTTATTTTCAAGGAGATACTCCAACCCC
65 AT-ATCGATTTCTCACAATCGGGGATACTCCAACCCAGTTATTTCCAAGGAGATACTCCAACCCC
18958 GTTACTATCTCCAAAATATTAAATTTCTCAT
129 GTTA-TATCTCCAAAATATTAAATTTCTCAT
18989 CGGGAAATAT
Statistics
Matches: 138, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
156 2 0.01
157 8 0.06
158 87 0.63
159 41 0.30
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (159 bp):
ATCGAGGATACTCCAACCCCGTTATCTCCGAGGGAGATACTCCAACCCCAGCTTTATTCTTAAAA
TATCGATTTCTCACAATCGGGGATACTCCAACCCAGTTATTTCCAAGGAGATACTCCAACCCCGT
TATATCTCCAAAATATTAAATTTCTCATA
Found at i:20883 original size:52 final size:52
Alignment explanation
Indices: 20777--20892 Score: 171
Period size: 52 Copynumber: 2.2 Consensus size: 52
20767 TTTGCCTGCA
* * ***
20777 TGTATCGATACATCTGGGCAAATTTGCCTGTATGTATTGATACATTTTATAG
1 TGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATAG
20829 TGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA-AAGATCAG
1 TGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGAT-AG
20881 TGTATCGATACA
1 TGTATCGATACA
20893 ATGTATCGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 2 0.03
52 56 0.97
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (52 bp):
TGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATAG
Found at i:20899 original size:13 final size:13
Alignment explanation
Indices: 20881--20905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20871 CAAAGATCAG
20881 TGTATCGATACAA
1 TGTATCGATACAA
20894 TGTATCGATACA
1 TGTATCGATACA
20906 TTTTGGTAAT
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:22347 original size:19 final size:19
Alignment explanation
Indices: 22323--22388 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 19
22313 ATATAGTCGA
22323 AATGTATCGAAACAATTTT
1 AATGTATCGAAACAATTTT
22342 AATGTATC-AATAC------
1 AATGTATCGAA-ACAATTTT
*
22355 AATGTATCGATACAATTTT
1 AATGTATCGAAACAATTTT
*
22374 AATGTATCGATACAA
1 AATGTATCGAAACAA
22389 ATTGCATTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 16
0.69 0.02 0.29
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
18 2 0.05
19 25 0.66
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (19 bp):
AATGTATCGAAACAATTTT
Found at i:22360 original size:32 final size:32
Alignment explanation
Indices: 22323--22388 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
22313 ATATAGTCGA
22323 AATGTATCGAAACAATTTTAATGTATCAATAC
1 AATGTATCGAAACAATTTTAATGTATCAATAC
* *
22355 AATGTATCGATACAATTTTAATGTATCGATAC
1 AATGTATCGAAACAATTTTAATGTATCAATAC
22387 AA
1 AA
22389 ATTGCATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (32 bp):
AATGTATCGAAACAATTTTAATGTATCAATAC
Found at i:22399 original size:20 final size:20
Alignment explanation
Indices: 22354--22408 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
22344 TGTATCAATA
*
22354 CAATGTATCGATAC-AATTT
1 CAATGTATCGATACAAATTG
*
22373 TAATGTATCGATACAAATTG
1 CAATGTATCGATACAAATTG
*
22393 CATTGTATCGATACAA
1 CAATGTATCGATACAA
22409 TCTGGAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
CAATGTATCGATACAAATTG
Found at i:22435 original size:48 final size:48
Alignment explanation
Indices: 22375--22471 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
22365 TACAATTTTA
* *
22375 ATGTATCGATACAAATTGCATTGTATCGATACAATCTGGAAAACCCAG
1 ATGTATCGATACAAATTGCAATGTATCAATACAATCTGGAAAACCCAG
** * *
22423 ATGTATCGATACATTTTGCAATGTATCAATACATTCTGGAAAATCCAG
1 ATGTATCGATACAAATTGCAATGTATCAATACAATCTGGAAAACCCAG
22471 A
1 A
22472 AGTGCCTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (48 bp):
ATGTATCGATACAAATTGCAATGTATCAATACAATCTGGAAAACCCAG
Found at i:25538 original size:77 final size:77
Alignment explanation
Indices: 25411--25567 Score: 235
Period size: 77 Copynumber: 2.0 Consensus size: 77
25401 ACAAGATTTT
* * * *
25411 TCCTAAACAACTTAGATAGTATGTTTATATTTGCATGTCCTAACCTTCTATTCCAA-AGACAAAG
1 TCCTAAACAACTTAGAAAGTATGCTCATATTTGCATGTCCTAACCTTCTATGCCAATA-ACAAAG
25475 TAAGTCATTGTTA
65 TAAGTCATTGTTA
* * *
25488 TCCTAGACAACTTAGAAAGTATGCTCATATTTGCATGTCCTAACCTTCTATGCCAATACCAAGGT
1 TCCTAAACAACTTAGAAAGTATGCTCATATTTGCATGTCCTAACCTTCTATGCCAATAACAAAGT
25553 AAGTCATTGTTA
66 AAGTCATTGTTA
25565 TCC
1 TCC
25568 ACAATAAAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
77 71 0.99
78 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (77 bp):
TCCTAAACAACTTAGAAAGTATGCTCATATTTGCATGTCCTAACCTTCTATGCCAATAACAAAGT
AAGTCATTGTTA
Found at i:28248 original size:144 final size:144
Alignment explanation
Indices: 27988--28278 Score: 555
Period size: 144 Copynumber: 2.0 Consensus size: 144
27978 CCAATTGATT
27988 ACCATAATTCACTAATCGAATTGTTACCTTTAAGGCAAAGGTATAACCTTACAACACTATCTTTC
1 ACCATAATTCACTAATCGAATTGTTACCTTTAAGGCAAAGGTATAACCTTACAACACTATCTTTC
* *
28053 AAGGCTAAGATAGAACCTCTCAATCACTCCGATAATTATACATGAAATTCTTGAGTGATTGTTCC
66 AAGGCTAAGATAGAACCTCTCAATCACTCCGAGAATTATACATGAAATTCTTGACTGATTGTTCC
28118 CAAGGTTGAACACA
131 CAAGGTTGAACACA
28132 ACCATAATTCACTAATCGAATTGTTACCTTTAAGGCAAAGGTATAACCTTACAACACTATCTTTC
1 ACCATAATTCACTAATCGAATTGTTACCTTTAAGGCAAAGGTATAACCTTACAACACTATCTTTC
*
28197 AAGGCTAAGATATAACCTCTCAATCACTCCGAGAATTATACATGAAATTCTTGACTGATTGTTCC
66 AAGGCTAAGATAGAACCTCTCAATCACTCCGAGAATTATACATGAAATTCTTGACTGATTGTTCC
28262 CAAGGTTGAACACA
131 CAAGGTTGAACACA
28276 ACC
1 ACC
28279 TTTTATAGCA
Statistics
Matches: 144, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
144 144 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (144 bp):
ACCATAATTCACTAATCGAATTGTTACCTTTAAGGCAAAGGTATAACCTTACAACACTATCTTTC
AAGGCTAAGATAGAACCTCTCAATCACTCCGAGAATTATACATGAAATTCTTGACTGATTGTTCC
CAAGGTTGAACACA
Found at i:28736 original size:13 final size:13
Alignment explanation
Indices: 28718--28751 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28708 TAGTTATATG
*
28718 TATTGATACTATA
1 TATTGATACAATA
*
28731 TATTGATACAATG
1 TATTGATACAATA
28744 TATTGATA
1 TATTGATA
28752 TAGTCGAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (13 bp):
TATTGATACAATA
Found at i:28770 original size:65 final size:65
Alignment explanation
Indices: 28666--28790 Score: 232
Period size: 65 Copynumber: 1.9 Consensus size: 65
28656 TTTAATCATG
*
28666 TATTGATACAATGAATTGATATAGTCGAAGGGTAGCTACTACTAGTTATATGTATTGATACTATA
1 TATTGATACAATGAATTGATATAGTCGAAGGGTAGCTACTACTAGTTATATGTATCGATACTATA
*
28731 TATTGATACAATGTATTGATATAGTCGAAGGGTAGCTACTACTAGTTATATGTATCGATA
1 TATTGATACAATGAATTGATATAGTCGAAGGGTAGCTACTACTAGTTATATGTATCGATA
28791 TATTTCATAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (65 bp):
TATTGATACAATGAATTGATATAGTCGAAGGGTAGCTACTACTAGTTATATGTATCGATACTATA
Found at i:31027 original size:163 final size:162
Alignment explanation
Indices: 30608--31215 Score: 562
Period size: 163 Copynumber: 3.7 Consensus size: 162
30598 TCACTTTTTA
* * * * * **
30608 TTAATTTTTTATATTTCTATAGGGATCTGTAGGGATATAAAAGATTTCAAAATTTTTTCGTATCT
1 TTAATCTTTTATATTCCTAT-GGGGTCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCGTATCT
* *
30673 TTTTGAGTTTCCATTAAGGTACGAAATGGTATTTTTCGAAAATAAATAAATTAATAAAATTAAAT
65 TTTTGAGTTTCCATTAAAGTACGAAATGATATTTTT-GAAAATAAAT--A--AATAAAATTAAAT
* * *
30738 TAATACTTTCATAATTGAA-ATAAATATTAATCATTT-TTCT
125 TAACACTTTCATCA-TCAAGATAAAT-TTAATC-TTTCTT-T
* * * * **
30778 TT--TTTTTTATATTCCTATGAGGGTCTGT-GAGGTATAAAAGATTTTAAAAACTTTTTATATCT
1 TTAATCTTTTATATTCCTATG-GGGTCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCGTATCT
* * * * *
30840 TTTCGAGTTTCCATTAAGGTACGAAATGGTATTTTTTAAAATAAGTAAATAAAATTAAATTAACA
65 TTTTGAGTTTCCATTAAAGTACGAAATGATATTTTTGAAAATAAATAAATAAAATTAAATTAACA
*
30905 CTTTCATCACCAAGATAAATTTTAATCTTTCTTT
130 CTTTCATCATCAAGATAAA-TTTAATCTTTCTTT
* * * *
30939 TTAATCTTTTATATGCCTATGGGCTCCATAGGGGTATAAAAGATTTCAAAAACTTTTCGTATCTC
1 TTAATCTTTTATATTCCTATGGGGTCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCGTATCTT
* * * * * *
31004 TTTGGGCTTT-CATTAAAGTACGAAATGATACTTTTAAAAATAAACAAATTAAAGTAAATTAACA
66 TTTGAG-TTTCCATTAAAGTACGAAATGATATTTTTGAAAATAAATAAATAAAATTAAATTAACA
* **
31068 CTTTCA-CAATCGAGAT-AA---AATC-ACCTTT
130 CTTTCATC-ATCAAGATAAATTTAATCTTTCTTT
* * *
31096 TTAATCTTTTATATTTCTATGGAGGTCCGTAAGGGTATAAAA-AGTTTCAAAAACTCTTCGTAT-
1 TTAATCTTTTATATTCCTATGG-GGTCCGTAGGGGTATAAAAGA-TTTCAAAAACTTTTCGTATC
* *
31159 TTTTTTAGGTTTTCATTAAAGTACGAAATGATATTTTTGAAAA-AAATTAAATCAAAA
64 TTTTTGA-GTTTCCATTAAAGTACGAAATGATATTTTTGAAAATAAA-TAAAT-AAAA
31216 ATATAAAATT
Statistics
Matches: 370, Mismatches: 53, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
157 35 0.09
158 71 0.19
159 3 0.01
161 8 0.02
162 46 0.12
163 108 0.29
164 4 0.01
166 8 0.02
167 63 0.17
168 22 0.06
170 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (162 bp):
TTAATCTTTTATATTCCTATGGGGTCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCGTATCTT
TTTGAGTTTCCATTAAAGTACGAAATGATATTTTTGAAAATAAATAAATAAAATTAAATTAACAC
TTTCATCATCAAGATAAATTTAATCTTTCTTT
Found at i:31709 original size:22 final size:23
Alignment explanation
Indices: 31667--31710 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
31657 ATGTAATTAT
*
31667 ATTTAAAATATGACATTCAATAA
1 ATTTAAAATATGAAATTCAATAA
*
31690 ATTTAAAAT-TTAAATTCAATA
1 ATTTAAAATATGAAATTCAATA
31711 TTTGCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (23 bp):
ATTTAAAATATGAAATTCAATAA
Found at i:34525 original size:16 final size:15
Alignment explanation
Indices: 34486--34542 Score: 62
Period size: 14 Copynumber: 3.7 Consensus size: 15
34476 GATAAATGTA
*
34486 TCTTTTATTCATTTT
1 TCTTTTATTTATTTT
**
34501 T-AATTATTTATTTT
1 TCTTTTATTTATTTT
34515 TCTATTTATTTTATTTT
1 TCT-TTTA-TTTATTTT
34532 TCTTTTATTTA
1 TCTTTTATTTA
34543 AAGTTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 11 0.32
15 5 0.15
16 7 0.21
17 11 0.32
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTTTATTTATTTT
Found at i:34529 original size:17 final size:16
Alignment explanation
Indices: 34507--34541 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
34497 TTTTTAATTA
34507 TTTATTTTTCTATTTAT
1 TTTATTTTTCT-TTTAT
34524 TTTATTTTTCTTTTAT
1 TTTATTTTTCTTTTAT
34540 TT
1 TT
34542 AAAGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTTTTCTTTTAT
Found at i:34677 original size:28 final size:28
Alignment explanation
Indices: 34616--34677 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
34606 AATTAAATTC
* * * **
34616 TAATTAAGTTATATTTTTTTTATAGTTC
1 TAATTAAGTTATATTCTATTTAAAGTAA
34644 TAATTAAGTTATATTCTATTTAAAGTAA
1 TAATTAAGTTATATTCTATTTAAAGTAA
*
34672 TTATTA
1 TAATTA
34678 TATATTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (28 bp):
TAATTAAGTTATATTCTATTTAAAGTAA
Found at i:36554 original size:19 final size:19
Alignment explanation
Indices: 36506--36580 Score: 107
Period size: 19 Copynumber: 3.9 Consensus size: 19
36496 ACTGCCAGTT
36506 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAA-TGA
36525 TCCATGTATCGATACAATGA
1 T-CATGTATCGATACAATGA
*
36545 TCACGTATCGATACAATGA
1 TCATGTATCGATACAATGA
*
36564 TCATTTATCGATACAAT
1 TCATGTATCGATACAAT
36581 ATATCATACA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 35 0.69
20 16 0.31
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:42194 original size:52 final size:51
Alignment explanation
Indices: 42116--42264 Score: 208
Period size: 52 Copynumber: 2.9 Consensus size: 51
42106 CGAAATATGA
* *
42116 AAATTTTCTTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
42168 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
42220 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
42265 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:42271 original size:13 final size:13
Alignment explanation
Indices: 42253--42277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42243 CAAAGATCAG
42253 TGTATCGATACAA
1 TGTATCGATACAA
42266 TGTATCGATACA
1 TGTATCGATACA
42278 TTTAAGTGAT
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:42345 original size:20 final size:20
Alignment explanation
Indices: 42320--42373 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
42310 TAGCTTGAAT
42320 TGTATCGATACAAAAAAATA
1 TGTATCGATACAAAAAAATA
* ***
42340 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAAAAATA
42360 TGTATCGATACAAA
1 TGTATCGATACAAA
42374 TCGTTGAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (20 bp):
TGTATCGATACAAAAAAATA
Found at i:43253 original size:55 final size:52
Alignment explanation
Indices: 43170--43462 Score: 285
Period size: 48 Copynumber: 5.9 Consensus size: 52
43160 GAGAAGTGAT
* * * * * *
43170 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-G-A
* * * *
43224 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
43277 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * * *
43320 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
43370 -AAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT-AA-A-GG-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
43417 CAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
43463 AAGAGACGCC
Statistics
Matches: 203, Mismatches: 25, Indels: 27
0.80 0.10 0.11
Matches are distributed among these distances:
43 38 0.19
44 1 0.00
46 1 0.00
47 2 0.01
48 41 0.20
49 40 0.20
51 1 0.00
52 32 0.16
53 6 0.03
54 5 0.02
55 36 0.18
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
Found at i:43338 original size:43 final size:43
Alignment explanation
Indices: 43277--43462 Score: 219
Period size: 43 Copynumber: 4.1 Consensus size: 43
43267 TAAAGATGGA
43277 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
43320 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T---T
* *
43367 ATGAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT
1 A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
43412 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT
1 --A---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
43460 AAA
1 AAA
43463 AAGAGACGCC
Statistics
Matches: 121, Mismatches: 13, Indels: 18
0.80 0.09 0.12
Matches are distributed among these distances:
43 40 0.33
44 1 0.01
45 1 0.01
46 1 0.01
47 3 0.02
48 40 0.33
49 35 0.29
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:43407 original size:92 final size:95
Alignment explanation
Indices: 43223--43462 Score: 324
Period size: 97 Copynumber: 2.5 Consensus size: 95
43213 AAAGATGAGA
* *
43223 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG-AAAGGTGCCAA
*
43288 TATGCTGATTCAAGGCCAGCTATATTGGACTT
64 TATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
43320 -AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G-AAGGTGCCAATA
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATA
*
43382 TGCTGATTTAAGGCCAGCGATATTGGACTT
66 TGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
43412 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 -AA---AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
43463 AAGAGACGCC
Statistics
Matches: 128, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
92 40 0.31
94 2 0.02
95 40 0.31
96 5 0.04
97 41 0.32
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.26
Consensus pattern (95 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATA
TGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:43539 original size:28 final size:28
Alignment explanation
Indices: 43482--43605 Score: 135
Period size: 28 Copynumber: 4.3 Consensus size: 28
43472 CACCAACTTG
*
43482 TGTGGGCTTTTGAGAGGTTTG-CA-TCAACT
1 TGTGGGCTTTTGA-AGG-TTGCCACT-GACT
* *
43511 TGTGTGCTTTTGAAGGTTGCTACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
43539 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
43567 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
43597 TGTGGGCTT
1 TGTGGGCTT
43606 AAAAAGAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
27 3 0.04
28 43 0.52
29 13 0.16
30 23 0.28
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.37
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:43590 original size:30 final size:30
Alignment explanation
Indices: 43508--43842 Score: 188
Period size: 29 Copynumber: 11.1 Consensus size: 30
43498 GTTTGCATCA
* * *
43508 ACTTGTGTGCTTTTG--AAGGTTGCTACTG
1 ACTTGTGGGCTTTTGAAAAGGATGCCACTG
*
43536 ACTTGTGGGCTTTT--AAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGATGCCACTG
* *
43564 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGATGCCACTG
** * *
43594 ACTTGTGGGCTTAAAAAGAAAAAGAGTGCTA-TAG
1 ACTTGTGGGCTT---TTGAAAAGGA-TGCCACT-G
* * ** * * *
43628 AGTTGTGAGCTTACAAAAGAAAAAGAGTGTCACGG
1 ACTTGTGGGCTT----TTGAAAAGGA-TGCCACTG
* * * * *
43663 AGTTGTAGACTTTGGAAAA-GATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGATGCCACTG
** *
43692 ACTTGTGGGCTTCAGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGATGCCACTG
* * *
43722 ATTTGTGGGC-TTTG--AAGGTTACCACTG
1 ACTTGTGGGCTTTTGAAAAGGATGCCACTG
**
43749 ACTTGTGGGCTTTTGAAAAAAAAATGCCACTG
1 ACTTGTGGGCTTTTG--AAAAGGATGCCACTG
*
43781 ACTTGTGGGC-TTTGAAAATGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGATGCCACTG
* *
43810 ACTTATGGAC-TTTGAAAAGGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGATGCCACTG
43839 ACTT
1 ACTT
43843 ATGAACTTTT
Statistics
Matches: 246, Mismatches: 45, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
27 20 0.08
28 43 0.17
29 65 0.26
30 43 0.17
31 9 0.04
32 19 0.08
33 7 0.03
34 14 0.06
35 26 0.11
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (30 bp):
ACTTGTGGGCTTTTGAAAAGGATGCCACTG
Found at i:43735 original size:59 final size:57
Alignment explanation
Indices: 43672--43842 Score: 173
Period size: 59 Copynumber: 2.9 Consensus size: 57
43662 GAGTTGTAGA
* * *
43672 CTTTGGAAAAGATGCCACCGACTTGTGGGCTTCAGAAAAGGGTGCCACTGATTTGTGGG
1 CTTT-GAAAAGATGCCACTGACTTGTGGGCTT-AGAAAAGGATGCCACTGACTTGTGGG
* * * * **
43731 CTTTG-AAGGTTACCACTGACTTGTGGGCTTTTGAAAAAAAAATGCCACTGACTTGTGGG
1 CTTTGAAAAGATGCCACTGACTTGTGGGC--TT-AGAAAAGGATGCCACTGACTTGTGGG
* * *
43790 CTTTGAAAATGATGCCACTGACTTATGGACTTTGAAAAGGATGCCACTGACTT
1 CTTTGAAAA-GATGCCACTGACTTGTGGGCTTAGAAAAGGATGCCACTGACTT
43843 ATGAACTTTT
Statistics
Matches: 89, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
57 19 0.21
58 18 0.20
59 34 0.38
60 2 0.02
61 16 0.18
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (57 bp):
CTTTGAAAAGATGCCACTGACTTGTGGGCTTAGAAAAGGATGCCACTGACTTGTGGG
Found at i:45237 original size:1 final size:1
Alignment explanation
Indices: 45231--45295 Score: 67
Period size: 1 Copynumber: 65.0 Consensus size: 1
45221 CATCCGGACC
* * * * * * *
45231 TTTTTTTTTATTTTTTTGTTTTTTTTTTGTTTTTGTTTTTTTTTGTTTTGTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
45296 GTGGAGGACG
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.02, C:0.00, G:0.09, T:0.89
Consensus pattern (1 bp):
T
Found at i:45252 original size:16 final size:15
Alignment explanation
Indices: 45233--45297 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 15
45223 TCCGGACCTT
45233 TTTTTTTATTTTTTTG
1 TTTTTTT-TTTTTTTG
45249 TTTTTTTTTTGTTTTTG
1 -TTTTTTTTT-TTTTTG
*
45266 TTTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTG
45281 TTTTGTTTTTTTTTTG
1 TTTT-TTTTTTTTTTG
45297 T
1 T
45298 GGAGGACGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
15 9 0.20
16 22 0.50
17 13 0.30
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:45296 original size:21 final size:19
Alignment explanation
Indices: 45231--45295 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 19
45221 CATCCGGACC
* *
45231 TTTTTTTTTATTTTTTTGT
1 TTTTTTTTTGTTTTTTTTT
45250 TTTTTTTTTGTTTTTGTTTT
1 TTTTTTTTTGTTTTT-TTTT
*
45270 TTTTTGTTTTGTTTTGTTTT
1 TTTTT-TTTTGTTTTTTTTT
45290 TTTTTT
1 TTTTTT
45296 GTGGAGGACG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 15 0.37
20 17 0.41
21 9 0.22
ACGTcount: A:0.02, C:0.00, G:0.09, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTGTTTTTTTTT
Found at i:45297 original size:21 final size:19
Alignment explanation
Indices: 45231--45295 Score: 85
Period size: 21 Copynumber: 3.3 Consensus size: 19
45221 CATCCGGACC
* *
45231 TTTTTTTTTATTTTTTTGT
1 TTTTTTTTTGTTTTTTTTT
45250 TTTTTTTTTGTTTTTGTTTT
1 TTTTTTTTTGTTTTT-TTTT
45270 TTTTTGTTTTGTTTTGTTTTT
1 TTTTT-TTTTGTTTT-TTTTT
45291 TTTTT
1 TTTTT
45296 GTGGAGGACG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.34
20 8 0.20
21 18 0.44
22 1 0.02
ACGTcount: A:0.02, C:0.00, G:0.09, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTGTTTTTTTTT
Found at i:59138 original size:52 final size:52
Alignment explanation
Indices: 59060--59208 Score: 212
Period size: 52 Copynumber: 2.9 Consensus size: 52
59050 CGAAATATGA
* *
59060 AAATTTGCTTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
* *
59112 AAATTTGCCTGCATGTATCGATACATT-ATAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGA-ATAGTGTATCGATACATCTGGGC
**
59164 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAAT-AGTGTATCGATACA
59209 ATATATCGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
Found at i:59282 original size:33 final size:33
Alignment explanation
Indices: 59245--59307 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
59235 GCTTGAATTG
59245 TATCGATACAAAAAAATATGTATCGATACATTA
1 TATCGATACAAAAAAATATGTATCGATACATTA
* ***
59278 TATCGATACAACACTTTATGTATCGATACA
1 TATCGATACAAAAAAATATGTATCGATACA
59308 AATTGTTGAA
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:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (33 bp):
TATCGATACAAAAAAATATGTATCGATACATTA
Found at i:59736 original size:20 final size:20
Alignment explanation
Indices: 59696--59736 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
59686 GGTTTTCCAG
*
59696 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTCAAGA
* *
59716 ATGTATCGATATATTCTAGA
1 ATGTATCGATACATTCAAGA
59736 A
1 A
59737 AATTTTTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTCAAGA
Found at i:64207 original size:9 final size:9
Alignment explanation
Indices: 64193--64226 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
64183 TCCGAGTCAC
64193 CATCATTAT
1 CATCATTAT
64202 CATCATTAT
1 CATCATTAT
64211 CATC-TTCAT
1 CATCATT-AT
64220 CATCATT
1 CATCATT
64227 GATGGTTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (9 bp):
CATCATTAT
Found at i:65906 original size:19 final size:19
Alignment explanation
Indices: 65862--65935 Score: 94
Period size: 20 Copynumber: 3.8 Consensus size: 19
65852 ACTGCCAGTT
* *
65862 TCATGTATCGATACAGTTGT
1 TCATGTATCGATACA-ATGA
65882 TCATGTATCGATACAATGA
1 TCATGTATCGATACAATGA
*
65901 TCATGTATCGATACAAAGCA
1 TCATGTATCGATACAATG-A
*
65921 TAATGTATCGATACA
1 TCATGTATCGATACA
65936 TCTGGGTGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 19 0.39
20 30 0.61
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:66602 original size:281 final size:282
Alignment explanation
Indices: 66224--66731 Score: 783
Period size: 281 Copynumber: 1.8 Consensus size: 282
66214 AGATCCTAAC
** * *
66224 AATAATTTATTTTTTAAAAAATTAATAATTTATATAGGATAAAACAAAAACAAATTCAAAAGATT
1 AATAATTTATCCTTTAAAAAATGAATAATTTATATAGGACAAAACAAAAACAAATTCAAAAGATT
* * * *
66289 GCAAAGCTTGGGATCGAAATCCTAATATCTTAAATTAAAAATCACTCTGTCAACAAATCAT-TCA
66 GCAAAGCTTGAGATCAAAATCCTAACATCTTAAATTAAAAATCACTCTATCAACAAATCATGT-A
* ** *
66353 ACAG-TTGTTTACTAGTTATTATATTTTCTATAGATATTTTAGTCATTAATTTTGAATTAAAAGC
130 A-AGATTGTTGACTAGTTATTATATTTTCTATAGATATTTTAGTCAAGAATTTTGAAATAAAAGC
66417 TTTTTTG-CTTGATATATTTATTTTAGTTAGGGATAATTAGGCAGCAGGATAGAAGTGAGGATTG
194 -TTTTTGCCTTGATATATTTATTTTAGTTAGGGATAATTAGGCAGCAGGATAGAAGTGAGGATTG
66481 CGTTGATTATTAATATTTGTATAAA
258 CGTTGATTATTAATATTTGTATAAA
* * *
66506 AATAATTTATCCTTTAAAAAA-GAATAATTTATTTAAGG-CAAAACGAAAACAAATTCAAAAGCT
1 AATAATTTATCCTTTAAAAAATGAATAATTTATAT-AGGACAAAACAAAAACAAATTCAAAAGAT
66569 TGCAAAGCTTGAGATCAAAATCCTAACATCTTAAATTAAAAATCACTCTATCAACAAATCATGTA
65 TGCAAAGCTTGAGATCAAAATCCTAACATCTTAAATTAAAAATCACTCTATCAACAAATCATGTA
* *
66634 ATGATTGTTGAGTAGTTATTATATTTTCTATAGATATTTTAGTCAAGAATTTTGAAATAAAAGCT
130 AAGATTGTTGACTAGTTATTATATTTTCTATAGATATTTTAGTCAAGAATTTTGAAATAAAAGCT
*
66699 TTTTGCCTTGATATGTTTATTTTAGTTAGGGAT
195 TTTTGCCTTGATATATTTATTTTAGTTAGGGAT
66732 GCCAATGGAG
Statistics
Matches: 204, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
280 7 0.03
281 174 0.85
282 23 0.11
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (282 bp):
AATAATTTATCCTTTAAAAAATGAATAATTTATATAGGACAAAACAAAAACAAATTCAAAAGATT
GCAAAGCTTGAGATCAAAATCCTAACATCTTAAATTAAAAATCACTCTATCAACAAATCATGTAA
AGATTGTTGACTAGTTATTATATTTTCTATAGATATTTTAGTCAAGAATTTTGAAATAAAAGCTT
TTTGCCTTGATATATTTATTTTAGTTAGGGATAATTAGGCAGCAGGATAGAAGTGAGGATTGCGT
TGATTATTAATATTTGTATAAA
Found at i:69809 original size:15 final size:14
Alignment explanation
Indices: 69789--69819 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
69779 ATGAGAATAA
69789 TAAAATTATTTTATT
1 TAAAATTATTTT-TT
69804 TAAAATTATTTTTT
1 TAAAATTATTTTTT
69818 TA
1 TA
69820 CTACAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TAAAATTATTTTTT
Found at i:69869 original size:20 final size:20
Alignment explanation
Indices: 69844--69881 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
69834 TTTATCTTTT
*
69844 TAATTTAAAATATCAAATCA
1 TAATTTAAAATATAAAATCA
*
69864 TAATTTTAAATATAAAAT
1 TAATTTAAAATATAAAAT
69882 TAAAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATTTAAAATATAAAATCA
Found at i:69888 original size:20 final size:20
Alignment explanation
Indices: 69845--69890 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
69835 TTATCTTTTT
* * *
69845 AATTTAAAATATCAAATCAT
1 AATTTTAAATATAAAATCAA
*
69865 AATTTTAAATATAAAATTAA
1 AATTTTAAATATAAAATCAA
69885 AATTTT
1 AATTTT
69891 TTACTCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTTAAATATAAAATCAA
Found at i:70468 original size:20 final size:20
Alignment explanation
Indices: 70443--70545 Score: 69
Period size: 20 Copynumber: 5.3 Consensus size: 20
70433 AATATAGTAC
70443 ATATAAAATTATTAAATATA
1 ATATAAAATTATTAAATATA
* *
70463 ATATAACATAATATAAATATA
1 ATATAAAATTAT-TAAATATA
*
70484 TGATTTAAAA-T-TT--ATATA
1 --ATATAAAATTATTAAATATA
70502 ATAT-AAATTATT-AATAT-
1 ATATAAAATTATTAAATATA
70519 ATA-AAAATTAATATAAATATA
1 ATATAAAATT-AT-TAAATATA
*
70540 AAATAA
1 ATATAA
70546 TTTAAATACG
Statistics
Matches: 64, Mismatches: 7, Indels: 22
0.69 0.08 0.24
Matches are distributed among these distances:
15 3 0.05
16 4 0.06
17 10 0.16
18 11 0.17
19 1 0.02
20 16 0.25
21 11 0.17
22 2 0.03
23 6 0.09
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (20 bp):
ATATAAAATTATTAAATATA
Found at i:70518 original size:18 final size:18
Alignment explanation
Indices: 70443--70541 Score: 57
Period size: 18 Copynumber: 5.4 Consensus size: 18
70433 AATATAGTAC
70443 ATATAAAATTATTAAATATA
1 ATAT-AAATTATT-AATATA
*
70463 ATATAACATAATATAAATATA
1 ATATAA-AT--TATTAATATA
* *
70484 TGATTTAAA--ATTTATATA
1 --ATATAAATTATTAATATA
70502 ATATAAATTATTAATAT-
1 ATATAAATTATTAATATA
70519 ATA-AAA--ATTAATATAA
1 ATATAAATTATTAATAT-A
70535 ATATAAA
1 ATATAAA
70542 ATAATTTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 23
0.68 0.07 0.25
Matches are distributed among these distances:
14 8 0.13
16 12 0.19
17 6 0.10
18 14 0.22
19 2 0.03
20 6 0.10
21 6 0.10
22 4 0.06
23 5 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (18 bp):
ATATAAATTATTAATATA
Found at i:70551 original size:16 final size:18
Alignment explanation
Indices: 70512--70553 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
70502 ATATAAATTA
70512 TTAATATATAAAAATTAAT
1 TTAA-ATATAAAAATTAAT
*
70531 ATAAATAT-AAAA-TAAT
1 TTAAATATAAAAATTAAT
70547 TTAAATA
1 TTAAATA
70554 CGATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 10 0.48
17 4 0.19
18 4 0.19
19 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAATATAAAAATTAAT
Found at i:71911 original size:32 final size:31
Alignment explanation
Indices: 71850--71915 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
71840 TAGATTTACT
* *
71850 AAATAAAAATATAAAAGAATAAATAAAAAATC
1 AAATAAAAATACAAAAGAAGAAATAAAAAA-C
* *
71882 AAATAAAAATACAAAAGAAGAAGTTAAAAAC
1 AAATAAAAATACAAAAGAAGAAATAAAAAAC
71913 AAA
1 AAA
71916 AAGGAATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 4 0.13
32 26 0.87
ACGTcount: A:0.74, C:0.05, G:0.06, T:0.15
Consensus pattern (31 bp):
AAATAAAAATACAAAAGAAGAAATAAAAAAC
Found at i:78446 original size:20 final size:20
Alignment explanation
Indices: 78421--78475 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
78411 ATTTGCCTGC
78421 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
78441 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
*
78461 ATGTATCCATACATT
1 ATGTATCGATACATT
78476 TGGGTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:78525 original size:20 final size:21
Alignment explanation
Indices: 78500--78544 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
78490 AAAATTTATT
78500 GATACAATG-AATAATGTATC
1 GATACAATGCAATAATGTATC
* * *
78520 GATACATTGCAATCATGTATT
1 GATACAATGCAATAATGTATC
78541 GATA
1 GATA
78545 TATTCACTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (21 bp):
GATACAATGCAATAATGTATC
Found at i:78539 original size:21 final size:21
Alignment explanation
Indices: 78500--78566 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 21
78490 AAAATTTATT
*
78500 GATACAATG-AATAATGTATC
1 GATACATTGCAATAATGTATC
* *
78520 GATACATTGCAATCATGTATT
1 GATACATTGCAATAATGTATC
* * * *
78541 GATATATT-CACTTATATATC
1 GATACATTGCAATAATGTATC
78561 GATACA
1 GATACA
78567 ATTTTTTCGA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (21 bp):
GATACATTGCAATAATGTATC
Found at i:78632 original size:20 final size:21
Alignment explanation
Indices: 78607--78657 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
78597 CATGGTCCAG
* *
78607 TATCGATACATTCATTTA-TA
1 TATCGATACATTAACTTATTA
*
78627 TATCGATACATTAACTTATTG
1 TATCGATACATTAACTTATTA
78648 TATCGATACA
1 TATCGATACA
78658 AATTATAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (21 bp):
TATCGATACATTAACTTATTA
Found at i:82393 original size:12 final size:12
Alignment explanation
Indices: 82376--82409 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
82366 ATGCTGGAAA
82376 TTTTATGACATG
1 TTTTATGACATG
82388 TTTTATGACATG
1 TTTTATGACATG
**
82400 GGTTATGACA
1 TTTTATGACA
82410 AAGATGCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (12 bp):
TTTTATGACATG
Found at i:83485 original size:52 final size:51
Alignment explanation
Indices: 83361--83485 Score: 162
Period size: 52 Copynumber: 2.4 Consensus size: 51
83351 ATTGAAACAT
* *
83361 TGAAGAATATATCGATAC-ATTTGGGTCAAAACCCAGAATATATCGATACAA
1 TGAAAAATATATCGAT-CTATTTGGGTAAAAACCCAGAATATATCGATACAA
* ** * *
83412 TGAAAAATGTATTAATATATTTGGGTTAAAAACCCATAATATATCGATACAA
1 TGAAAAATATATCGATCTATTTGGG-TAAAAACCCAGAATATATCGATACAA
83464 TGAAAAATATATCGATCTATTT
1 TGAAAAATATATCGATCTATTT
83486 CCTTTCTAGA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
51 19 0.31
52 42 0.69
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (51 bp):
TGAAAAATATATCGATCTATTTGGGTAAAAACCCAGAATATATCGATACAA
Found at i:84415 original size:52 final size:52
Alignment explanation
Indices: 84304--84549 Score: 246
Period size: 52 Copynumber: 4.7 Consensus size: 52
84294 AGATTTCTTG
* * * * * * **
84304 GCCAATATGCAGATTTAAAGCCTA-CGACACTGGACTTAAAGATGATAAGGGT
1 GCCAATATACTGATTT-AAGGCTAGCGACATTAGACTTAAAGATGAGAAGAAT
* *
84356 GCCAATATGCTGATTTAAGGCTAGCGACATTAGACTTAAATATGAGAAGAAT
1 GCCAATATACTGATTTAAGGCTAGCGACATTAGACTTAAAGATGAGAAGAAT
* * * * *
84408 GCTAATATACTGGTTTAAGGCCAGCGACATCAGACTTAAAAATGAGAA-AAGT
1 GCCAATATACTGATTTAAGGCTAGCGACATTAGACTTAAAGATGAGAAGAA-T
* * * * *
84460 GCCAATGTACTAATTCAAGGCTAGCGACATTGGACTTAAAGGTGAGAAGAAT
1 GCCAATATACTGATTTAAGGCTAGCGACATTAGACTTAAAGATGAGAAGAAT
* *
84512 GCCAATGTACTGATTTAAGGCTA-CTAACATTAGACTTA
1 GCCAATATACTGATTTAAGGCTAGC-GACATTAGACTTA
84550 GAAGGAAATG
Statistics
Matches: 162, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
51 9 0.06
52 151 0.93
53 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (52 bp):
GCCAATATACTGATTTAAGGCTAGCGACATTAGACTTAAAGATGAGAAGAAT
Found at i:84881 original size:99 final size:95
Alignment explanation
Indices: 84710--85335 Score: 266
Period size: 96 Copynumber: 6.5 Consensus size: 95
84700 AAAAGATGGT
* * * * * * *
84710 ACTTGTGTGGGCTTTGAAAGGGTTGCCATCGACTTGTGTGGGTTTTTTAAAAAGGTTGCTACCAA
1 ACTTGTGTAGGCTTTGAAAGGGTTGCCACCGACTTATGTGGGCTTTTGAAAAAGGATGCCACCAA
* * **
84775 TTTGTGTGAGCTTTATAAAAAGGGTTGCCACTG
66 CTGGTGTGAGC-TT-T-AAAAGGGTTGCCACAA
* * **
84808 ACTTGTGTAGGCTTTTGAGAGGGTTGTCACCGACTTATGTGGGCTTTTGAAAAAGGATGCCACTG
1 ACTTGTGTAGGC-TTTGAAAGGGTTGCCACCGACTTATGTGGGCTTTTGAAAAAGGATGCCACCA
* *
84873 ACTGGTGTGGGCTTTGAAAGGGTTGCCACAA
65 ACTGGTGTGAGCTTTAAAAGGGTTGCCACAA
* ***** ** * * * *
84904 ACTTGTGT-GTGTTTTTGAAAAAAAAGCCACTAACTTGTGTGGGC-TTT-AAAAGGGTTGCCACT
1 ACTTGTGTAG-G-CTTTGAAAGGGTTGCCACCGACTTATGTGGGCTTTTGAAAAAGGATGCCACC
* ** ** * * *
84966 GACTTCTGTGGATTTTTGAAAAAGATTGCCACCA
64 AACTGGTGT-GAGCTTT-AAAAGGGTTGCCACAA
** * * * ** *
85000 ACTTGTGTAGGCCTTAAAAAAGGGTTGCCATCGACTTGTGTGGGC-TTT-AAAAAAGATTATCAT
1 ACTTGTGTAGG-CTT-TGAAAGGGTTGCCACCGACTTATGTGGGCTTTTGAAAAAGGA-TGCCAC
* * * **
85063 CGACTTGTGTGGGCTTTAAAAAGGGTTGCCATGGA
63 CAACTGGTGTGAGCTTT-AAAAGGGTTGCCA-CAA
* * * * ** * * * *
85098 A-TTATG--GGCTTTTAAAAAAGGATGCCACTAACTTTTGTGGGC-TTT-AAAAGGGTTGCCACT
1 ACTTGTGTAGGC-TTT-GAAAGGGTTGCCACCGACTTATGTGGGCTTTTGAAAAAGGATGCCACC
* * * *
85158 GACTTGTGTGGGCTTTTAAAAAAGGGTTGCTAGC-A
64 AACTGGTGTGAGC-TTT--AAAAGGGTTGCCA-CAA
* * * * * * *
85193 ACTTGTGTAGGCTTTAAAAAGGGCTGCCATCAACTTTTGTGGGTTTTTGAAAAACGATGCCACCA
1 ACTTGTGTAGGCTTT-GAAAGGGTTGCCACCGACTTATGTGGGCTTTTGAAAAAGGATGCCACCA
* * * *
85258 ACTTGTATGGGCTTTAAAAGGGTTGCCACCA
65 ACTGGTGTGAGCTTTAAAAGGGTTGCCACAA
* * * *
85289 ACTTGTGTGGGCTTTTGAAAATGGTTACCACCGACTTGTGTGGGCTT
1 ACTTGTGTAGGC-TTTG-AAAGGGTTGCCACCGACTTATGTGGGCTT
85336 AAAAATGGTT
Statistics
Matches: 400, Mismatches: 107, Indels: 43
0.73 0.19 0.08
Matches are distributed among these distances:
94 37 0.09
95 48 0.12
96 107 0.27
97 100 0.25
98 35 0.09
99 73 0.18
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (95 bp):
ACTTGTGTAGGCTTTGAAAGGGTTGCCACCGACTTATGTGGGCTTTTGAAAAAGGATGCCACCAA
CTGGTGTGAGCTTTAAAAGGGTTGCCACAA
Found at i:84920 original size:64 final size:63
Alignment explanation
Indices: 84710--85359 Score: 444
Period size: 64 Copynumber: 10.1 Consensus size: 63
84700 AAAAGATGGT
* * * * * *
84710 ACTTGTGTGGGC-TTTG-AAAGGGTTGCCA-TCGACTTGTGTGGGTTTTTTAAAAAGGTTGCTAC
1 ACTTGTGTGGGCTTTTGAAAAAGGATGCCACT-AACTTGTGTGGG--CTTTAAAAGGGTTGCCA-
84772 CA
62 CA
* * * * * * * *
84774 ATTTGTGTGAGCTTTAT-AAAAAGGGTTGCCACTGACTTGTGTAGGCTTTTGAGAGGGTTGTCAC
1 ACTTGTGTGGGCTTT-TGAAAAA-GGATGCCACTAACTTGTGTGGGC-TTTAAAAGGGTTGCCA-
*
84838 CG
62 CA
* * * *
84840 ACTTATGTGGGCTTTTGAAAAAGGATGCCACTGACTGGTGTGGGCTTTGAAAGGGTTGCCACAA
1 ACTTGTGTGGGCTTTTGAAAAAGGATGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCAC-A
* * * * *
84904 ACTTGTGTGTGTTTTTGAAAAA-AAAGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCACTG
1 ACTTGTGTGGGCTTTTGAAAAAGGATGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCAC-A
* ** * * *
84967 ACTTCTGTGGATTTTTGAAAAA-GATTGCCACCAACTTGTGTAGGCCTTAAAAAAGGGTTGCCAT
1 ACTTGTGTGGGCTTTTGAAAAAGGA-TGCCACTAACTTGTGT-GGGCTT-TAAAAGGGTTGCCA-
*
85031 CG
62 CA
* ** *
85033 ACTTGTGTGGGC-TTT-AAAAAAGATTATCA-TCGACTTGTGTGGGCTTTAAAAAGGGTTGCCAT
1 ACTTGTGTGGGCTTTTGAAAAAGGA-TGCCACT-AACTTGTGTGGGCTTT-AAAAGGGTTGCCA-
*
85095 GGA
62 -CA
* * * *
85098 A--T-TATGGGCTTTTAAAAAAGGATGCCACTAACTTTTGTGGGCTTTAAAAGGGTTGCCACTG
1 ACTTGTGTGGGCTTTTGAAAAAGGATGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCAC-A
* * * * *
85159 ACTTGTGTGGGCTTTTAAAAAAGGGTTGCTAGC-AACTTGTGTAGGCTTTAAAAAGGGCTGCCAT
1 ACTTGTGTGGGCTTTTGAAAAA-GGATGCCA-CTAACTTGTGTGGGCTTT-AAAAGGGTTGCCA-
85223 CA
62 CA
* * * * *
85225 ACTTTTGTGGGTTTTTGAAAAACGATGCCACCAACTTGTATGGGCTTTAAAAGGGTTGCCACCA
1 ACTTGTGTGGGCTTTTGAAAAAGGATGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCA-CA
* * * ** * * *
85289 ACTTGTGTGGGCTTTTGAAAATGGTTACCACCGACTTGTGTGGGCTTAAAAATGGTTACCACTA
1 ACTTGTGTGGGCTTTTGAAAAAGGATGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCAC-A
85353 GACTTGT
1 -ACTTGT
85360 CAATTTTAAC
Statistics
Matches: 470, Mismatches: 86, Indels: 59
0.76 0.14 0.10
Matches are distributed among these distances:
61 1 0.00
62 19 0.04
63 78 0.17
64 170 0.36
65 91 0.19
66 89 0.19
67 21 0.04
68 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (63 bp):
ACTTGTGTGGGCTTTTGAAAAAGGATGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCACA
Found at i:84921 original size:32 final size:31
Alignment explanation
Indices: 84710--84986 Score: 151
Period size: 32 Copynumber: 8.6 Consensus size: 31
84700 AAAAGATGGT
**
84710 ACTTGTGTGGGCTTTGAAAGGGTTGCCA-TCG
1 ACTTGTGTGGTTTTTGAAAGGGTTGCCACT-G
* * * **
84741 ACTTGTGTGGGTTTTTTAAAAAGGTTGCTACCA
1 ACTTGTGT-GG-TTTTTGAAAGGGTTGCCACTG
* **
84774 ATTTGTGTGAGCTTTATAAAAAGGGTTGCCACTG
1 ACTTGTGTG-G-TTT-TTGAAAGGGTTGCCACTG
* * * *
84808 ACTTGTGTAGGCTTTTGAGAGGGTTGTCACCG
1 ACTTGTGT-GGTTTTTGAAAGGGTTGCCACTG
* * * *
84840 ACTTATGTGGGCTTTTGAAAAAGGATGCCACTG
1 ACTTGTGT-GGTTTTTG-AAAGGGTTGCCACTG
* ** **
84873 ACTGGTGTGGGCTTTGAAAGGGTTGCCACAA
1 ACTTGTGTGGTTTTTGAAAGGGTTGCCACTG
***** *
84904 ACTTGTGTGTGTTTTTGAAAAAAAAGCCACTA
1 ACTTGTGTG-GTTTTTGAAAGGGTTGCCACTG
** *
84936 ACTTGTGTGGGCTTTAAAAGGGTTGCCACTG
1 ACTTGTGTGGTTTTTGAAAGGGTTGCCACTG
*
84967 ACTTCTGTGGATTTTTGAAA
1 ACTTGTGTGG-TTTTTGAAA
84987 AAGATTGCCA
Statistics
Matches: 179, Mismatches: 58, Indels: 17
0.70 0.23 0.07
Matches are distributed among these distances:
31 49 0.27
32 66 0.37
33 42 0.23
34 21 0.12
35 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (31 bp):
ACTTGTGTGGTTTTTGAAAGGGTTGCCACTG
Found at i:85075 original size:192 final size:193
Alignment explanation
Indices: 84786--85309 Score: 533
Period size: 192 Copynumber: 2.7 Consensus size: 193
84776 TTGTGTGAGC
* ** *** * * * * * *
84786 TTTATAAAAAGGGTTGCCACTGACTTGTGTAGGCTTTTGAGAGGGTTGTCACCGACTTATGTGGG
1 TTTA-AAAAAGGATTGCCACCAACTTGTGTAGGCTTAAAAAAGGGCTGCCATCAACTTGTGTGGG
* * * * *
84851 -CTTTTGAAAAAGGATGCCACTGACTGGTGTGGGCTTTGAAAGGGTTGCCACAAACTTGTGTGTG
65 TC-TTTGAAAAAAGATACCACCGACTTGTGTGGGCTTTAAAAGGGTTGCCACAAACTTGTGTG-G
* *
84915 TTTTTGAAAAAA-AAGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCACTGACTTCTGTGGAT
128 CTTTTGAAAAAAGAAGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCACTGACTTCTGTGGAC
84979 T
193 T
* * *
84980 TTTGAAAAA-GATTGCCACCAACTTGTGTAGGCCTTAAAAAAGGGTTGCCATCGACTTGTGTGGG
1 TTTAAAAAAGGATTGCCACCAACTTGTGTAGG-CTTAAAAAAGGGCTGCCATCAACTTGTGTGGG
* * ** *
85044 -CTTT-AAAAAAGATTATCATCGACTTGTGTGGGCTTTAAAAAGGGTTGCCATGGAA-TTATG-G
65 TCTTTGAAAAAAGA-TACCACCGACTTGTGTGGGCTTT-AAAAGGGTTGCCA-CAAACTTGTGTG
* * *
85105 GCTTTT-AAAAAAGGATGCCACTAACTTTTGTGGGCTTTAAAAGGGTTGCCACTGACTTGTGTGG
127 GCTTTTGAAAAAA-GAAGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCACTGACTTCTGTGG
*
85169 GCT
191 ACT
* * * * *
85172 TTTAAAAAAGGGTTGCTAGCAACTTGTGTAGGCTTTAAAAAGGGCTGCCATCAACTTTTGTGGGT
1 TTTAAAAAAGGATTGCCACCAACTTGTGTAGGCTTAAAAAAGGGCTGCCATCAACTTGTGTGGGT
* * * * * *
85237 TTTTGAAAAACGATGCCACCAACTTGTATGGGCTTTAAAAGGGTTGCCACCAACTTGTGTGGGCT
66 CTTTGAAAAAAGATACCACCGACTTGTGTGGGCTTTAAAAGGGTTGCCACAAACTTGTGT-GGCT
85302 TTTGAAAA
130 TTTGAAAA
85310 TGGTTACCAC
Statistics
Matches: 272, Mismatches: 45, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
190 6 0.02
191 14 0.05
192 142 0.52
193 87 0.32
194 19 0.07
195 4 0.01
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (193 bp):
TTTAAAAAAGGATTGCCACCAACTTGTGTAGGCTTAAAAAAGGGCTGCCATCAACTTGTGTGGGT
CTTTGAAAAAAGATACCACCGACTTGTGTGGGCTTTAAAAGGGTTGCCACAAACTTGTGTGGCTT
TTGAAAAAAGAAGCCACTAACTTGTGTGGGCTTTAAAAGGGTTGCCACTGACTTCTGTGGACT
Found at i:85344 original size:31 final size:31
Alignment explanation
Indices: 84710--85359 Score: 281
Period size: 33 Copynumber: 20.2 Consensus size: 31
84700 AAAAGATGGT
** *
84710 ACTTGTGTGGGCTTTGAAAGGGTTGCCATCG
1 ACTTGTGTGGGCTTAAAAAGGGTTGCCACCG
* * *
84741 ACTTGTGTGGGTTTTTTAAAAA-GGTTGCTACCA
1 ACTTGTGTGGG---CTTAAAAAGGGTTGCCACCG
* * *
84774 ATTTGTGTGAGCTTTATAAAAAGGGTTGCCACTG
1 ACTTGTGTGGGC--T-TAAAAAGGGTTGCCACCG
* ** * *
84808 ACTTGTGTAGGCTTTTGAGAGGGTTGTCACCG
1 ACTTGTGTGGGC-TTAAAAAGGGTTGCCACCG
* * *
84840 ACTTATGTGGGCTTTTGAAAAA-GGATGCCACTG
1 ACTTGTGTGGGC--TT-AAAAAGGGTTGCCACCG
* ** **
84873 ACTGGTGTGGGCTTTGAAAGGGTTGCCACAA
1 ACTTGTGTGGGCTTAAAAAGGGTTGCCACCG
** *** **
84904 ACTTGTGTGTGTTTTTGAAAAA--AAAGCCACTA
1 ACTTGTGTG-G-GCTT-AAAAAGGGTTGCCACCG
* *
84936 ACTTGTGTGGGCTTTAAAAGGGTTGCCACTG
1 ACTTGTGTGGGCTTAAAAAGGGTTGCCACCG
* ** * *
84967 ACTTCTGTGGATTTTTGAAAAA-GATTGCCACCA
1 ACTTGTGTGG--GCTT-AAAAAGGGTTGCCACCG
* *
85000 ACTTGTGTAGGCCTTAAAAAAGGGTTGCCATCG
1 ACTTGTGT-GGGCTT-AAAAAGGGTTGCCACCG
* * ** *
85033 ACTTGTGTGGGCTTTAAAAAAGATTATCATCG
1 ACTTGTGTGGGC-TTAAAAAGGGTTGCCACCG
**
85065 ACTTGTGTGGGCTTTAAAAAGGGTTGCCATGG
1 ACTTGTGTGGGC-TTAAAAAGGGTTGCCACCG
* * * * **
85097 A-AT-TATGGGCTTTTAAAAAAGGATGCCACTA
1 ACTTGTGTGGGC--TTAAAAAGGGTTGCCACCG
* * *
85128 ACTTTTGTGGGCTTTAAAAGGGTTGCCACTG
1 ACTTGTGTGGGCTTAAAAAGGGTTGCCACCG
* * *
85159 ACTTGTGTGGGCTTTTAAAAAAGGGTTGCTAGCA
1 ACTTGTGTGGGC--TT-AAAAAGGGTTGCCACCG
* * * *
85193 ACTTGTGTAGGCTTTAAAAAGGGCTGCCATCA
1 ACTTGTGTGGGC-TTAAAAAGGGTTGCCACCG
* * * * *
85225 ACTTTTGTGGGTTTTTGAAAAA-CGATGCCACCA
1 ACTTGTGTGGG--CTT-AAAAAGGGTTGCCACCG
* * *
85258 ACTTGTATGGGCTTTAAAAGGGTTGCCACCA
1 ACTTGTGTGGGCTTAAAAAGGGTTGCCACCG
* * *
85289 ACTTGTGTGGGCTTTTGAAAATGGTTACCACCG
1 ACTTGTGTGGGC--TTAAAAAGGGTTGCCACCG
* * *
85322 ACTTGTGTGGGCTTAAAAATGGTTACCACTAG
1 ACTTGTGTGGGCTTAAAAAGGGTTGCCAC-CG
85354 ACTTGT
1 ACTTGT
85360 CAATTTTAAC
Statistics
Matches: 468, Mismatches: 117, Indels: 67
0.72 0.18 0.10
Matches are distributed among these distances:
29 4 0.01
30 15 0.03
31 126 0.27
32 122 0.26
33 140 0.30
34 61 0.13
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (31 bp):
ACTTGTGTGGGCTTAAAAAGGGTTGCCACCG
Done.