Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_400
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: 78897
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:4275 original size:30 final size:29
Alignment explanation
Indices: 4233--4295 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 29
4223 AAGTAGCCGG
4233 AGCTAGTTAAATCGCACACCTAGTGCCAA
1 AGCTAGTTAAATCGCACACCTAGTGCCAA
*
4262 AGCTAGTTTAAATCGCACACTTAGTGCCAA
1 AGCTAG-TTAAATCGCACACCTAGTGCCAA
4292 AGCT
1 AGCT
4296 TCCGATTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (29 bp):
AGCTAGTTAAATCGCACACCTAGTGCCAA
Found at i:6953 original size:21 final size:21
Alignment explanation
Indices: 6929--6973 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
6919 AATCCCCACA
6929 TGGTGTGTTGGTTGG-TATGGG
1 TGGTGTGTTGGTTGGAT-TGGG
6950 TGGTGTGTTGGTTGGATTGGG
1 TGGTGTGTTGGTTGGATTGGG
6971 TGG
1 TGG
6974 GTTACATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.04, C:0.00, G:0.53, T:0.42
Consensus pattern (21 bp):
TGGTGTGTTGGTTGGATTGGG
Found at i:29595 original size:19 final size:18
Alignment explanation
Indices: 29567--29614 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
29557 TAACCGAAAA
29567 AATAATAAATAAAATTAT
1 AATAATAAATAAAATTAT
29585 AATATATAAATAAAATTAT
1 AATA-ATAAATAAAATTAT
29604 AATACATAAAT
1 AATA-ATAAAT
29615 CCAAATACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATAAATAAAATTAT
Found at i:29856 original size:18 final size:18
Alignment explanation
Indices: 29781--29857 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 18
29771 TTTATTCAAA
* *
29781 TAATTCGTTTAATTCAGT
1 TAATTCGGTTAATTCGGT
* *
29799 TAATTTGGGTAATTCGAG-
1 TAATTCGGTTAATTCG-GT
** * **
29817 TAATTTAGTCAATTCGAC
1 TAATTCGGTTAATTCGGT
29835 TAATTCGGTTAATTCGGT
1 TAATTCGGTTAATTCGGT
29853 TAATT
1 TAATT
29858 TTATACTTTT
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
18 43 0.98
19 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGT
Found at i:29857 original size:27 final size:27
Alignment explanation
Indices: 29781--29857 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 27
29771 TTTATTCAAA
* * **
29781 TAATTCGTTTAATTCAGTTAATTTGGG
1 TAATTCGGTTAATTCAGTTAATTCGAC
* *
29808 TAATTCGAG-TAATTTAGTCAATTCGAC
1 TAATTCG-GTTAATTCAGTTAATTCGAC
*
29835 TAATTCGGTTAATTCGGTTAATT
1 TAATTCGGTTAATTCAGTTAATT
29858 TTATACTTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (27 bp):
TAATTCGGTTAATTCAGTTAATTCGAC
Found at i:31911 original size:43 final size:43
Alignment explanation
Indices: 31850--31936 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
31840 AAATATCCTT
31850 ACCTTCATTTCCTTCATTTTGTGTAGTAGTTAGCAACTTAGCA
1 ACCTTCATTTCCTTCATTTTGTGTAGTAGTTAGCAACTTAGCA
31893 ACCTTCATTTCCTTCATTTTGTGTAGTAGTTAGCAACTTAGCA
1 ACCTTCATTTCCTTCATTTTGTGTAGTAGTTAGCAACTTAGCA
31936 A
1 A
31937 TTGCTGTTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (43 bp):
ACCTTCATTTCCTTCATTTTGTGTAGTAGTTAGCAACTTAGCA
Found at i:39010 original size:48 final size:48
Alignment explanation
Indices: 38955--39174 Score: 233
Period size: 48 Copynumber: 4.6 Consensus size: 48
38945 GTGAATTGTC
* * *
38955 GATGCCATGTTCCAAACATGGCCTTACACTAGCTCACATGTCGAGGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAGGTT
* * * * * * *
39003 GATGCCATGTCCCACACATGGTCTTACACTAGCTCTCGTCTCAATGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAGGTT
* * * * *
39051 GATGCCATGGCCCAGACATGGTCTTACACTGGCTCTCATGTTGTGGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAGGTT
* * * * * **
39099 GATGCCATGTCTCAGACATGGTCTTACACTAGCGCACATATCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAGGTT
*
39147 GATGCCATGTCCCGGACATGGTCTTACA
1 GATGCCATGTCCCAGACATGGTCTTACA
39175 TTGGCTCTTA
Statistics
Matches: 139, Mismatches: 33, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 139 1.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAGGTT
Found at i:39118 original size:96 final size:96
Alignment explanation
Indices: 38951--39182 Score: 311
Period size: 96 Copynumber: 2.4 Consensus size: 96
38941 AAGGGTGAAT
* * * * *
38951 TGTCGATGCCATGTTCCAAACATGGCCTTACACTAGCTCACATGTCGAGGTTGATGCCATGTCCC
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGTCGAGGTTGATGCCATGTCCC
* * * *
39016 ACACATGGTCTTACACTAGCTCTCGTCTCAA
66 ACACATGGTCTTACACTAGCGCACATATCAA
* * * *
39047 TGTCGATGCCATGGCCCAGACATGGTCTTACACTGGCTCTCATGTTGTGGTTGATGCCATGTCTC
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGTCGAGGTTGATGCCATGTCCC
*
39112 AGACATGGTCTTACACTAGCGCACATATCAA
66 ACACATGGTCTTACACTAGCGCACATATCAA
* * *
39143 TGCCGATGCCATGTCCCGGACATGGTCTTACATTGGCTCT
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT
39183 TACAACATCG
Statistics
Matches: 118, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 118 1.00
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (96 bp):
TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGTCGAGGTTGATGCCATGTCCC
ACACATGGTCTTACACTAGCGCACATATCAA
Found at i:39218 original size:144 final size:143
Alignment explanation
Indices: 38954--39268 Score: 332
Period size: 144 Copynumber: 2.2 Consensus size: 143
38944 GGTGAATTGT
* * * * **
38954 CGATGCCATGT-TCCAAACATGGCCTTACACTAGCTCACATGTCGAGGTTGATGCCATGTCCCAC
1 CGATGCCATGTCT-CAAACATGGTCTTACACTAGCGCACATATCAAGGCCGATGCCATGTCCCAC
* * * *
39018 ACATGGTCTTACACTAGCTCTCGTCTCAATGTCGATGCCATGGCCCAGACATGGTCTTACACTGG
65 ACATGGTCTTACACTAGCTCTC-TCACAATGCCGATGCCATGGCCCAAACAAGGTCTTACACTGG
* * *
39083 CTCTCATGTTGTGGT
129 CTCTCATATCGTGGC
* * * **
39098 TGATGCCATGTCTCAGACATGGTCTTACACTAGCGCACATATCAATGCCGATGCCATGTCCCGGA
1 CGATGCCATGTCTCAAACATGGTCTTACACTAGCGCACATATCAAGGCCGATGCCATGTCCCACA
* * ** *
39163 CATGGTCTTACATTGGCTCT-T-ACAACATCGCCGATGCCATGTTCCAAACAAGGTCTTACATTG
66 CATGGTCTTACACTAGCTCTCTCAC-A-AT-GCCGATGCCATGGCCCAAACAAGGTCTTACACTG
39226 GCTCTCATATCGTGGC
128 GCTCTCATATCGTGGC
*
39242 CGACGCCATGTC-CTAAACATGGTCTTA
1 CGATGCCATGTCTC-AAACATGGTCTTA
39269 TGCTGGCACA
Statistics
Matches: 140, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
141 1 0.01
142 2 0.01
143 3 0.02
144 133 0.95
145 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (143 bp):
CGATGCCATGTCTCAAACATGGTCTTACACTAGCGCACATATCAAGGCCGATGCCATGTCCCACA
CATGGTCTTACACTAGCTCTCTCACAATGCCGATGCCATGGCCCAAACAAGGTCTTACACTGGCT
CTCATATCGTGGC
Found at i:39235 original size:96 final size:96
Alignment explanation
Indices: 39003--39268 Score: 257
Period size: 96 Copynumber: 2.8 Consensus size: 96
38993 TGTCGAGGTT
* * * * * *
39003 GATGCCATGTCCCACACATGGTCTTACACTAGCTCTCGTCTCAATGTCGATGCCATGGCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTCCCAGAC
***** * **
39068 ATGGTCTTACACTGGCTCTCATGTTGTGGTT
66 ATGGTCTTACACTGGCTCTCACAACATCGCC
* * * *
39099 GATGCCATG-TCTCAGACATGGTCTTACACTAGCGCACATATCAATGCCGATGCCATGTCCCGGA
1 GATGCCATGTTC-CAAACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTCCCAGA
* *
39163 CATGGTCTTACATTGGCTCTTACAACATCGCC
65 CATGGTCTTACACTGGCTCTCACAACATCGCC
* * * * * * *
39195 GATGCCATGTTCCAAACAAGGTCTTACATTGGCTCTCATATC-GTGGCCGACGCCATGTCCTAAA
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCAAT-GCCGATGCCATGTCCCAGA
39259 CATGGTCTTA
65 CATGGTCTTA
39269 TGCTGGCACA
Statistics
Matches: 137, Mismatches: 30, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
95 2 0.01
96 133 0.97
97 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (96 bp):
GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTGGCTCTCACAACATCGCC
Found at i:39244 original size:48 final size:48
Alignment explanation
Indices: 38954--39268 Score: 226
Period size: 48 Copynumber: 6.6 Consensus size: 48
38944 GGTGAATTGT
* * * *
38954 CGATGCCATGTTCCAAACATGGCCTTACACTAGCTCACATGTCGA-GGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATC-ATGGC
* * * * * *
39002 TGATGCCATGTCCCACACATGGTCTTACACTAGCTCTCGTCTCAAT-GT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATC-ATGGC
** * * * ** *
39050 CGATGCCATGGCCCAGACATGGTCTTACACTGGCTCTCATGTTGTGGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCATGGC
* * * *
39098 TGATGCCATG-TCTCAGACATGGTCTTACACTAGCGCACATATCAAT-GC
1 CGATGCCATGTTC-CAAACATGGTCTTACACTAGCTCTCATATC-ATGGC
* ** * * * * * *
39146 CGATGCCATGTCCCGGACATGGTCTTACATTGGCTCTTACAACATCGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCATGGC
* * * *
39194 CGATGCCATGTTCCAAACAAGGTCTTACATTGGCTCTCATATCGTGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCATGGC
*
39242 CGACGCCATG-TCCTAAACATGGTCTTA
1 CGATGCCATGTTCC-AAACATGGTCTTA
39269 TGCTGGCACA
Statistics
Matches: 214, Mismatches: 46, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
47 7 0.03
48 205 0.96
49 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCATGGC
Found at i:41185 original size:22 final size:22
Alignment explanation
Indices: 41159--41205 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
41149 AATATTAAAC
41159 TAAGTATGGTAAATAGACCATT
1 TAAGTATGGTAAATAGACCATT
41181 TAAGTATGGTAAATAGACCATT
1 TAAGTATGGTAAATAGACCATT
41203 TAA
1 TAA
41206 TGAGATAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.32
Consensus pattern (22 bp):
TAAGTATGGTAAATAGACCATT
Found at i:43321 original size:18 final size:17
Alignment explanation
Indices: 43298--43333 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
43288 TGAAAAAGGG
43298 TTGAATCCCGATTGAATA
1 TTGAATCCCGA-TGAATA
*
43316 TTGAATTCCGATGAATA
1 TTGAATCCCGATGAATA
43333 T
1 T
43334 ATAGGCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (17 bp):
TTGAATCCCGATGAATA
Found at i:53983 original size:46 final size:48
Alignment explanation
Indices: 53833--54152 Score: 268
Period size: 46 Copynumber: 6.8 Consensus size: 48
53823 TCACTGGTGT
* * *
53833 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCA-C-ATTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GGCATCGA-GATGA
* *
53879 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGA
* * * *
53927 GTGCTAGTGTAAGA-CATGTCTGGGACAT-ACATCGGCCTCGAGATGTA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATG-A
* *
53974 -AGCCAGTGTAAGA-CATGTCTGGGACAT-GCGTCGG-ATAG-GA-GA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGA
* * * * * *
54016 TGTGTCAGTGTAAGACCATGTCTAGGACATGGAATCGGCATGGATATGCGA
1 -GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGAT--GA
* * * *
54067 GAGCTAGTGTAAGACCATGTCTGAGACATGGCATCAGCCTCGATGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGA-GATGA
* * * *
54116 TAGCCAATGTAAGACCATGTCAGGGACATGGCTTCGG
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG
54153 AAACTTGCCA
Statistics
Matches: 218, Mismatches: 41, Indels: 27
0.76 0.14 0.09
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 13 0.06
45 15 0.07
46 61 0.28
47 35 0.16
48 21 0.10
49 33 0.15
50 34 0.16
51 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.23
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGA
Found at i:57583 original size:11 final size:11
Alignment explanation
Indices: 57567--57591 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
57557 TTCAATTCAA
57567 ATAATCAATAT
1 ATAATCAATAT
57578 ATAATCAATAT
1 ATAATCAATAT
57589 ATA
1 ATA
57592 TACCAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:57616 original size:15 final size:16
Alignment explanation
Indices: 57569--57618 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
57559 CAATTCAAAT
*
57569 AATCAATATATAA-TC
1 AATCAATATACAATTC
57584 AAT-ATATATACCAATTC
1 AATCA-ATATA-CAATTC
57601 AATCAATATA-AATTC
1 AATCAATATACAATTC
57616 AAT
1 AAT
57619 AAATTCATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 2 0.07
17 10 0.33
18 1 0.03
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (16 bp):
AATCAATATACAATTC
Found at i:57641 original size:24 final size:24
Alignment explanation
Indices: 57596--57642 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
57586 TATATATACC
57596 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
57620 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
57643 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:58314 original size:11 final size:11
Alignment explanation
Indices: 58298--58367 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
58288 ATCTTTCTCC
58298 TTTTCTTTCTT
1 TTTTCTTTCTT
58309 TTTTCTTTCTT
1 TTTTCTTTCTT
*
58320 TTTT-TTCCTT
1 TTTTCTTTCTT
*
58330 CTATTTCGTTTGTT
1 -T-TTTC-TTTCTT
*
58344 CTTTCTTTCTT
1 TTTTCTTTCTT
* *
58355 TTCTATTTCTT
1 TTTTCTTTCTT
58366 TT
1 TT
58368 ATTATTATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
10 5 0.11
11 31 0.66
12 7 0.15
14 4 0.09
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:58428 original size:13 final size:13
Alignment explanation
Indices: 58412--58463 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
58402 TAAGATTTAA
58412 TATTATATAATAT
1 TATTATATAATAT
58425 TATTATAT-ATAT
1 TATTATATAATAT
*
58437 TATTACTTTAA-AT
1 TATTA-TATAATAT
*
58450 TTTTATAATAATAT
1 TATTAT-ATAATAT
58464 ATACCTTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 10 0.31
13 19 0.59
14 3 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATATAATAT
Found at i:60433 original size:22 final size:22
Alignment explanation
Indices: 60399--60442 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
60389 CAAATTCAAA
* *
60399 TTAAATATTAAAACATTTAAAT
1 TTAAATATAAAAACATATAAAT
* *
60421 TTAATTATAAAAATATATAAAT
1 TTAAATATAAAAACATATAAAT
60443 GTTATTAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAATATAAAAACATATAAAT
Found at i:64436 original size:46 final size:45
Alignment explanation
Indices: 64383--64553 Score: 182
Period size: 46 Copynumber: 3.7 Consensus size: 45
64373 TCTTGTAGTT
* * *
64383 GATGCATGTCCCAGACATTTCTTACACTGGCT-TACATCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATAT-GAGGCC
* * * * * *
64429 GATGCATGTTCTAGACATGTCTTACACTAGCTCTCATTTAAATGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAT-GAGGCC
*
64475 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-ATGAGGCC
*
64523 AATGCATGTCCCAGACATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
64554 ACACAATTAA
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
46 52 0.50
47 27 0.26
48 24 0.23
49 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATGAGGCC
Found at i:64502 original size:94 final size:92
Alignment explanation
Indices: 64382--64553 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 92
64372 ATCTTGTAGT
* * * * * *
64382 TGATGCATGTCCCAGACATTTCTTACACTGGCT-TACAT-CTCGAGGCCGATGCATGTTCTAGAC
1 TGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATAAT-GAGGCCAATGCATGTCCCAGAC
64445 ATGTCTTACACTAGCTCTCATTTAAATGC
64 ATGTCTTACACTAGCTCTCATTTAAATGC
*
64474 TGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCCAATGCATGTCCCAGAC
1 TGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAATGAGGCCAATGCATGTCCCAGAC
64539 ATGTCTTACACTAGC
64 ATGTCTTACACTAGC
64554 ACACAATTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
92 5 0.07
93 14 0.20
94 48 0.70
95 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (92 bp):
TGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAATGAGGCCAATGCATGTCCCAGACAT
GTCTTACACTAGCTCTCATTTAAATGC
Found at i:66454 original size:34 final size:34
Alignment explanation
Indices: 66372--66459 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 34
66362 AGGAATGAAC
*
66372 TATATACAT-AATAGATTTAAAAATATATATACA
1 TATATAAATAAATAGATTTAAAAATATATATACA
*
66405 TATATATATAAATAGATTTAAAAGA-A-AT-TACA
1 TATATAAATAAATAGATTTAAAA-ATATATATACA
*
66437 TATATAAAATAACATAGAATTAA
1 TATAT-AAATAA-ATAGATTTAA
66460 TAATGTACAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
32 9 0.19
33 15 0.31
34 23 0.48
35 1 0.02
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (34 bp):
TATATAAATAAATAGATTTAAAAATATATATACA
Found at i:66781 original size:15 final size:16
Alignment explanation
Indices: 66751--66786 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
66741 AATTAAAGGG
66751 ATAATTGATAAATGAA
1 ATAATTGATAAATGAA
*
66767 ATAATTGA-AATTGAA
1 ATAATTGATAAATGAA
66782 ATAAT
1 ATAAT
66787 GACCAAAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (16 bp):
ATAATTGATAAATGAA
Found at i:67725 original size:25 final size:23
Alignment explanation
Indices: 67691--67736 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
67681 TAAAGAAATG
67691 GAAAAAAAAAGAGAAAGAAAATGAT
1 GAAAAAAAAAGA-AAA-AAAATGAT
*
67716 GAAAACAAAAGAAAAAAAATG
1 GAAAAAAAAAGAAAAAAAATG
67737 TGTCCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (23 bp):
GAAAAAAAAAGAAAAAAAATGAT
Found at i:68369 original size:37 final size:37
Alignment explanation
Indices: 68328--68415 Score: 176
Period size: 37 Copynumber: 2.4 Consensus size: 37
68318 AACATAGACA
68328 TGTATGTTCGGCCACATGAATAAGTACATAAGTTATG
1 TGTATGTTCGGCCACATGAATAAGTACATAAGTTATG
68365 TGTATGTTCGGCCACATGAATAAGTACATAAGTTATG
1 TGTATGTTCGGCCACATGAATAAGTACATAAGTTATG
68402 TGTATGTTCGGCCA
1 TGTATGTTCGGCCA
68416 TAGGTAGCCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (37 bp):
TGTATGTTCGGCCACATGAATAAGTACATAAGTTATG
Found at i:69205 original size:40 final size:40
Alignment explanation
Indices: 69014--69198 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
69004 TCGAATGATG
* * * *
69014 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
69054 TCCGGACTAAGAT-CCGAAGGCATTTTTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
69094 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
69133 TTCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
69174 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
69199 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 9 0.07
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:69220 original size:79 final size:78
Alignment explanation
Indices: 69051--69231 Score: 179
Period size: 79 Copynumber: 2.3 Consensus size: 78
69041 CTAAGTGACC
* * **
69051 ATATCCGGACTAAGATCC-GAAGGCATTTTTGCGAGTTACTAATTTCGGGCTAAGCCCGAAGGCA
1 ATATCCGG-TTAAG-TCCTGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCA
**
69115 TTGGTGCGAGTTACT
64 TTGGAACGAGTTACT
* * *
69130 AAATTCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGC
1 ATA-TCCGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGC
*
69194 ATTTGAACGAG-TAGCT
63 ATTGGAACGAGTTA-CT
* *
69210 ATATCCGGTTAAATTCTGAAGG
1 ATATCCGGTTAAGTCCTGAAGG
69232 TACGTGATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
78 5 0.06
79 53 0.64
80 25 0.30
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (78 bp):
ATATCCGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATT
GGAACGAGTTACT
Found at i:75801 original size:23 final size:24
Alignment explanation
Indices: 75763--75809 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
75753 TAATAAAGAA
*
75763 ATGAAAAAAAAGAGAAAGAAAATG
1 ATGAAAAAAAAGAGAAAAAAAATG
*
75787 ATGAAAACAAA-AGAAAAAAAATG
1 ATGAAAAAAAAGAGAAAAAAAATG
75810 TGTCCATCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (24 bp):
ATGAAAAAAAAGAGAAAAAAAATG
Found at i:76464 original size:37 final size:36
Alignment explanation
Indices: 76399--76484 Score: 156
Period size: 37 Copynumber: 2.4 Consensus size: 36
76389 AACATAGACA
76399 TGTATGTTCGG-CACATGATAAGTACATAAGTTATG
1 TGTATGTTCGGCCACATGATAAGTACATAAGTTATG
76434 TGTATGTTCGGCCACATGAATAAGTACATAAGTTATG
1 TGTATGTTCGGCCACATG-ATAAGTACATAAGTTATG
76471 TGTATGTTCGGCCA
1 TGTATGTTCGGCCA
76485 TAGGTAGCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 11 0.22
36 6 0.12
37 32 0.65
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (36 bp):
TGTATGTTCGGCCACATGATAAGTACATAAGTTATG
Found at i:77164 original size:40 final size:39
Alignment explanation
Indices: 77080--77263 Score: 194
Period size: 39 Copynumber: 4.6 Consensus size: 39
77070 TCGAATGATG
* * * *
77080 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
77120 TCCGGACTAAGATCTGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
77160 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
77199 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
77239 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
77264 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 67 0.55
40 47 0.39
41 8 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:77270 original size:79 final size:78
Alignment explanation
Indices: 77135--77286 Score: 193
Period size: 78 Copynumber: 1.9 Consensus size: 78
77125 ACTAAGATCT
* **
77135 GAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTA-CTAAA
1 GAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAG-TAGCTAAA
77199 TCCGGGTTAAGTCCC
65 TCC-GGTTAAGTCCC
* * *
77214 GAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTAT
1 GAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTAGCTAA
77277 ATCCGGTTAA
64 ATCCGGTTAA
77287 ATTCGAAGGT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
77 2 0.03
78 31 0.48
79 31 0.48
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (78 bp):
GAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTAAAT
CCGGTTAAGTCCC
Done.