Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015020.1 Kokia drynarioides strain JFW-HI SEQ_130064, whole genome shotgun sequence
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: 1341705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 344 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1249923 original size:21 final size:21
Alignment explanation
Indices: 1249899--1249953 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1249889 TGAATTACAT
*
1249899 GGGTGGACACACGGGCATGTG
1 GGGTAGACACACGGGCATGTG
* * *
1249920 GGGTAGCCACATGGGCATGTT
1 GGGTAGACACACGGGCATGTG
* *
1249941 GGATAGCCACACG
1 GGGTAGACACACG
1249954 AGTGTGTGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.40, T:0.16
Consensus pattern (21 bp):
GGGTAGACACACGGGCATGTG
Found at i:1254917 original size:34 final size:34
Alignment explanation
Indices: 1254878--1255024 Score: 190
Period size: 34 Copynumber: 4.3 Consensus size: 34
1254868 TGTTACAGTT
* * *
1254878 TTTGGTGTGTT-GTATGAATTAACCCTTACGAGCA
1 TTTGGTGTGTTGGT-TGAACTAGCTCTTACGAGCA
*
1254912 TTTGGTGTGTTGGATTG-ACTAGCTTTTACGAGCA
1 TTTGGTGTGTTGG-TTGAACTAGCTCTTACGAGCA
1254946 TTTGGTGTGTTGGTTGAACTAGCTCTTACGAGCA
1 TTTGGTGTGTTGGTTGAACTAGCTCTTACGAGCA
** * *
1254980 TTTATTGTGTTGGTTGGACTATCTCTTACGAGCA
1 TTTGGTGTGTTGGTTGAACTAGCTCTTACGAGCA
1255014 TTTGGTGTGTT
1 TTTGGTGTGTT
1255025 CGATGGTTAA
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
33 3 0.03
34 92 0.93
35 3 0.03
36 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.27, T:0.42
Consensus pattern (34 bp):
TTTGGTGTGTTGGTTGAACTAGCTCTTACGAGCA
Found at i:1255820 original size:21 final size:21
Alignment explanation
Indices: 1255796--1255851 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
1255786 GCACACGAGT
**
1255796 ATGTGGGGTAGCCACATGGGC
1 ATGTGGGGTAGCCACACAGGC
* *
1255817 ATGTTGGGTGGCCACACAGGC
1 ATGTGGGGTAGCCACACAGGC
* *
1255838 GTGTGGGATAGCCA
1 ATGTGGGGTAGCCA
1255852 TACAACCATG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.41, T:0.20
Consensus pattern (21 bp):
ATGTGGGGTAGCCACACAGGC
Found at i:1256527 original size:184 final size:185
Alignment explanation
Indices: 1256179--1256547 Score: 481
Period size: 184 Copynumber: 2.0 Consensus size: 185
1256169 GTTTTTAAAA
** * *
1256179 AAAGAAGTTTATAAGCTTGTTTTTAGCACTATTTTCACAAAATATGTTTTTCGGATATGAACTGG
1 AAAGAAGTTTATAAGCTTGTTTTTAGCACTATTTTCACAAAATATGTTTTTCAAAGATGAACTAG
* *
1256244 GTCTCGCAACCTCACTTGTGAACCCAGCACGCGAAACGTTATAAAATTATCAACGTCTTGCTAGT
66 GTCTCGCAACCTCACCTGCGAACCCAG-ACGCGAAACGTTATAAAATTATCAACGTCTTGCTAGT
* * * * *
1256309 GGCTCATTGAATGATGCACATATGGTCAAAAACCATCTACGGTGAAGGCTGTCTAG
130 GGCCCACTAAATGATACACATATGATCAAAAACCATCTACGGTGAAGGCTGTCTAG
* * * * * * *
1256365 AAAGAATTTTGTAAGTTTGTTTTTAGCACTGTTTTCATAAAATATGTTTTTCAAAGGTGAATTAG
1 AAAGAAGTTTATAAGCTTGTTTTTAGCACTATTTTCACAAAATATGTTTTTCAAAGATGAACTAG
* * * * * *
1256430 GTCTCGCAACCTTACCTGCGAACCTAG-CGCTAAATGTTTTAAAATTATCAACCT-TCTGCTAGT
66 GTCTCGCAACCTCACCTGCGAACCCAGACGCGAAACGTTATAAAATTATCAACGTCT-TGCTAGT
*
1256493 GGCCCACTAAATGATACACATATGATCAAAAACCATCTATGGTGAAGGCTGTCTA
130 GGCCCACTAAATGATACACATATGATCAAAAACCATCTACGGTGAAGGCTGTCTA
1256548 AGAAGATGAT
Statistics
Matches: 157, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
183 1 0.01
184 79 0.50
186 77 0.49
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (185 bp):
AAAGAAGTTTATAAGCTTGTTTTTAGCACTATTTTCACAAAATATGTTTTTCAAAGATGAACTAG
GTCTCGCAACCTCACCTGCGAACCCAGACGCGAAACGTTATAAAATTATCAACGTCTTGCTAGTG
GCCCACTAAATGATACACATATGATCAAAAACCATCTACGGTGAAGGCTGTCTAG
Found at i:1259298 original size:106 final size:107
Alignment explanation
Indices: 1259170--1259390 Score: 372
Period size: 107 Copynumber: 2.1 Consensus size: 107
1259160 TTTACTGAAT
* * *
1259170 ATAATTTAACGTAATTATAATTATTAACTATAATGATTTCGTTAAATATT-AAAACATGGAAGTT
1 ATAATTTAAAGTAATTATAATTATTAACTATAATGATTTCGTTAAATATTAAAAAAATGGAAATT
1259234 AATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
66 AATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
* *
1259276 ATAATTTAAATTAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAAAAATGGAAATT
1 ATAATTTAAAGTAATTATAATTATTAACTATAATGATTTCGTTAAATATTAAAAAAATGGAAATT
*
1259341 AATATCCTTTTGGAAATGATATAATGTTTTAATAAACCTTCC
66 AATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
1259383 ATATATTT
1 ATA-ATTT
1259391 CTTTAAAGGA
Statistics
Matches: 107, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
106 47 0.44
107 56 0.52
108 4 0.04
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (107 bp):
ATAATTTAAAGTAATTATAATTATTAACTATAATGATTTCGTTAAATATTAAAAAAATGGAAATT
AATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
Found at i:1259303 original size:13 final size:13
Alignment explanation
Indices: 1259285--1259309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1259275 CATAATTTAA
1259285 ATTAATTATAATT
1 ATTAATTATAATT
1259298 ATTAATTATAAT
1 ATTAATTATAAT
1259310 GATTTCGTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTAATTATAATT
Found at i:1259459 original size:123 final size:124
Alignment explanation
Indices: 1259317--1259688 Score: 516
Period size: 122 Copynumber: 3.0 Consensus size: 124
1259307 AATGATTTCG
*
1259317 TTAAATATTAAAAAAATGGAAATTAATATCCTTTTGGAAATGATATAATGTTTTAATAAACCTTC
1 TTAAATATTAAAAACATGGAAATTAATATCCTTTTGGAAATGATATAATGTTTTAATAAACCTTC
* *
1259382 CATATATTTCTTTAAAGGAATATTTCCATTTTAATATTAGATATTAAATAAAAAG-AAT
66 CATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTAAATAAAAAGAAAA
* * * *
1259440 TTGAATATTAAAAACATGGAAATTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAATCTTT
1 TTAAATATTAAAAACATGGAAATTAATATCCTTTTGGAAATGATATAATGTTTTAATAAACCTTC
* * * *
1259505 TACATATTT-TTTAAAGGAATATTTTCATTTTAATATGAGATATTATAT-AAAAGAAAA
66 CATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTAAATAAAAAGAAAA
* *
1259562 TTAAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAATGATATAATGTTTTAATAAACCGTC
1 TTAAATATTAAAAACATGGAAATTAATATCCTTTTGGAAATGATATAATGTTTTAATAAACCTTC
* * *
1259627 CATATATTTCTCTAAAGATATATATATATTTCCATTTTAATATGATATATTAAAATAAAAAG
66 CATATATTTCTTTAAAG-----GA-ATATTTCCATTTTAATATGAGATATT-AAATAAAAAG
1259689 GAAAGATAAT
Statistics
Matches: 215, Mismatches: 24, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
121 5 0.02
122 104 0.48
123 73 0.34
128 1 0.00
129 24 0.11
130 3 0.01
131 5 0.02
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (124 bp):
TTAAATATTAAAAACATGGAAATTAATATCCTTTTGGAAATGATATAATGTTTTAATAAACCTTC
CATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTAAATAAAAAGAAAA
Found at i:1263139 original size:25 final size:25
Alignment explanation
Indices: 1263111--1263199 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
1263101 AATTTTACGA
*
1263111 AAGAGCGATATTCTATTTGGCTCGT
1 AAGAGCGATATTCTATTTGGCTTGT
* ** *
1263136 AAGAGCAATATTCTAAATTCTGAATTGA
1 AAGAGCGATATTCT--ATT-TGGCTTGT
* *
1263164 AAGAGCGATATTCTGTATGGCTTGT
1 AAGAGCGATATTCTATTTGGCTTGT
1263189 AAGAGC-ATATT
1 AAGAGCGATATT
1263200 TCTGTCTAGA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
24 5 0.10
25 24 0.48
26 1 0.02
27 3 0.06
28 17 0.34
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (25 bp):
AAGAGCGATATTCTATTTGGCTTGT
Found at i:1263944 original size:21 final size:20
Alignment explanation
Indices: 1263920--1263976 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
1263910 TCTAGAGTTT
1263920 GTTGTATCGGTAGAA-ACATGA
1 GTTGTATCGGTAGAAGA-AT-A
* *
1263941 GTTGTTTTGGTAGAAGTAATA
1 GTTGTATCGGTAGAAG-AATA
*
1263962 CTTGTATCGGTAGAA
1 GTTGTATCGGTAGAA
1263977 CCTCCACAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 26 0.90
22 2 0.07
23 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (20 bp):
GTTGTATCGGTAGAAGAATA
Found at i:1276831 original size:21 final size:21
Alignment explanation
Indices: 1276807--1276848 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1276797 ATGATCAAAT
*
1276807 GAAGG-AGAAGGATGAAGAAGA
1 GAAGGTAGAAAGA-GAAGAAGA
1276828 GAAGGTAGAAAGAGAAGAAGA
1 GAAGGTAGAAAGAGAAGAAGA
1276849 AAATGAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.40, T:0.05
Consensus pattern (21 bp):
GAAGGTAGAAAGAGAAGAAGA
Found at i:1281194 original size:14 final size:15
Alignment explanation
Indices: 1281175--1281206 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1281165 TGAAAATTCC
1281175 TTATAG-CAAGGGAG
1 TTATAGACAAGGGAG
1281189 TTATAGACAAGGGAG
1 TTATAGACAAGGGAG
1281204 TTA
1 TTA
1281207 CAACAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.25
Consensus pattern (15 bp):
TTATAGACAAGGGAG
Found at i:1293750 original size:20 final size:19
Alignment explanation
Indices: 1293716--1293753 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1293706 GCAAGAAGTG
*
1293716 ATTTAAATTTCATGATTTA
1 ATTTAAATTTAATGATTTA
1293735 ATTTAGAATTTAATGATTT
1 ATTTA-AATTTAATGATTT
1293754 GTTGATTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.53
Consensus pattern (19 bp):
ATTTAAATTTAATGATTTA
Found at i:1293998 original size:25 final size:25
Alignment explanation
Indices: 1293955--1294046 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
1293945 CTCTGAATTC
* *
1293955 TGGCTCGAAAGAGTAATATTTTGTT
1 TGGCTCGAAAGAGCAATATTTTATT
* * * *
1293980 TGGCTCGTAAGAGCGATATTCTAAATCC
1 TGGCTCGAAAGAGCAATATT-T-TAT-T
* *
1294008 TGGCTCGAAAGATCAATATTCTATT
1 TGGCTCGAAAGAGCAATATTTTATT
*
1294033 TGGCTCGTAAGAGC
1 TGGCTCGAAAGAGC
1294047 GTATTTCTGT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
25 29 0.58
26 3 0.06
27 1 0.02
28 17 0.34
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (25 bp):
TGGCTCGAAAGAGCAATATTTTATT
Found at i:1294054 original size:25 final size:26
Alignment explanation
Indices: 1293978--1294051 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 26
1293968 TAATATTTTG
1293978 TTTGGCTCGTAAGAGCGATATTCTAAA
1 TTTGGCTCGTAAGAGCGATATTCT-AA
* * * *
1294005 TCCTGGCTCGAAAGATCAATATTCT-A
1 T-TTGGCTCGTAAGAGCGATATTCTAA
1294031 TTTGGCTCGTAAGAGCG-TATT
1 TTTGGCTCGTAAGAGCGATATT
1294052 TCTGTCTGGA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
24 4 0.11
25 12 0.32
26 2 0.05
27 1 0.03
28 19 0.50
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (26 bp):
TTTGGCTCGTAAGAGCGATATTCTAA
Found at i:1296677 original size:96 final size:96
Alignment explanation
Indices: 1296511--1296702 Score: 330
Period size: 96 Copynumber: 2.0 Consensus size: 96
1296501 ACCTTAATTA
1296511 ACCCACCTAAAGGGGTTAAACCAATAGGGTGCAAGTGGGTTTTCAAGAAGAAAATCGACATGGAT
1 ACCCACCTAAAGGGGTTAAACCAATAGGGTGCAAGTGGGTTTTCAAGAAGAAAATCGACATGGAT
**
1296576 AGTAATGTACAAACATACAAAGGGTGATTGG
66 AGTAATGTACAAACATACAAAGCATGATTGG
* * *
1296607 ACCCACCTGAAGGGGTTAAACCCATAGGGTGCAAGTGGGTTTTCATGAAGAAAATCGACATGGAT
1 ACCCACCTAAAGGGGTTAAACCAATAGGGTGCAAGTGGGTTTTCAAGAAGAAAATCGACATGGAT
*
1296672 GGTAATGTACAAACATACAAAGCATGATTGG
66 AGTAATGTACAAACATACAAAGCATGATTGG
1296703 TTGCTAAAGG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 90 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (96 bp):
ACCCACCTAAAGGGGTTAAACCAATAGGGTGCAAGTGGGTTTTCAAGAAGAAAATCGACATGGAT
AGTAATGTACAAACATACAAAGCATGATTGG
Found at i:1299337 original size:123 final size:125
Alignment explanation
Indices: 1299204--1299451 Score: 358
Period size: 123 Copynumber: 2.0 Consensus size: 125
1299194 GATTTCGTTA
*
1299204 AATATTAAAACATGGAAGTTAATATCCTTTTGGAAAATATATAATGTTTTAATAAACCTTCCATA
1 AATATTAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCATA
* * * * *
1299269 TATTTCTTTAACG-GA-ATATTTCCATTTTAATATGAGATATT-ATATAAAAGGAAATTG
66 TATCTCTCTAAAGAGATATATTTCCATTTTAATATGAGATATTAAAATAAAACGAAATTG
* * *
1299326 AATATTAAAAACATGGAAGTTAATATCTTTTTGGAAAGGATATAATGTTTTAATAAACTTTCCAT
1 AATATT-AAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
*
1299391 ATATCTCTCTAAAGATATATATATTTCCATTTTAATATGAGATATTAAAATAAAACGAAAT
65 ATATCTCTCTAAAG--AGATATATTTCCATTTTAATATGAGATATTAAAATAAAACGAAAT
1299452 GATATTTTTC
Statistics
Matches: 110, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
122 6 0.05
123 65 0.59
126 1 0.01
127 26 0.24
128 12 0.11
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (125 bp):
AATATTAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCATA
TATCTCTCTAAAGAGATATATTTCCATTTTAATATGAGATATTAAAATAAAACGAAATTG
Found at i:1304975 original size:23 final size:24
Alignment explanation
Indices: 1304928--1304982 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
1304918 CGTATATGAC
1304928 CTATAGTTCCAAACCTCTTCTATAT
1 CTAT-GTTCCAAACCTCTTCTATAT
*
1304953 CTATGTTCCTAACCT-TTCTATAT
1 CTATGTTCCAAACCTCTTCTATAT
*
1304976 CAATGTT
1 CTATGTT
1304983 ATTTATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 14 0.50
24 10 0.36
25 4 0.14
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.44
Consensus pattern (24 bp):
CTATGTTCCAAACCTCTTCTATAT
Found at i:1308979 original size:41 final size:41
Alignment explanation
Indices: 1308891--1308991 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 41
1308881 TCGTGACTCA
* * *
1308891 GAATGAGCAA-GAGAATATGTTAAAGGAAGACTCATGTCACG
1 GAATGAG-AATGAGATTATGATAAAGGAAGACTCATGCCACG
* **
1308932 GGATGAGAATGAGATTATGATAAAGGAAGACTCATGCCTTG
1 GAATGAGAATGAGATTATGATAAAGGAAGACTCATGCCACG
**
1308973 GAATGAGTGTGAGATTATG
1 GAATGAGAATGAGATTATG
1308992 TTTAAAAGGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 2 0.04
41 48 0.96
ACGTcount: A:0.38, C:0.09, G:0.30, T:0.24
Consensus pattern (41 bp):
GAATGAGAATGAGATTATGATAAAGGAAGACTCATGCCACG
Found at i:1310894 original size:15 final size:17
Alignment explanation
Indices: 1310864--1310897 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1310854 GTGAAGAGGA
1310864 AGGAGGAGATGACGATG
1 AGGAGGAGATGACGATG
1310881 AGGA-GAGA-GACGATG
1 AGGAGGAGATGACGATG
1310896 AG
1 AG
1310898 ATGGATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 4 0.24
17 4 0.24
ACGTcount: A:0.38, C:0.06, G:0.47, T:0.09
Consensus pattern (17 bp):
AGGAGGAGATGACGATG
Found at i:1313760 original size:3 final size:3
Alignment explanation
Indices: 1313754--1313796 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1313744 GTTTTATAAC
1313754 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1313797 AAAAACCCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1325156 original size:381 final size:381
Alignment explanation
Indices: 1324449--1325204 Score: 1305
Period size: 381 Copynumber: 2.0 Consensus size: 381
1324439 TTACACTATT
* *
1324449 GTCCTCATCTGGCCAACCCTCATTACATTACTTTATCCCATCAAGTTGAGCTTTGTTGATGGTAT
1 GTCCTCATCTGGCCAACCCTCATTACATGACTTTATCCCATCAAGTTAAGCTTTGTTGATGGTAT
*
1324514 TAAAGTCCAAATCATCCCAATCGTTAGGACTTTTCTCCTATTAGAATTGGTTGACTAGAATTCTT
66 TAAAGTCCAAATCATCCCAATCGTTAGGACTTTTCTCCTATTAGAATTGGGTGACTAGAATTCTT
1324579 ATTAAGGTGGAGATTATTAGAATTGGGTGACTAGAATTCTTGTTAAAATAAAATTCAATGGTAAA
131 ATTAAGGTGGAGATTATTAGAATTGGGTGACTAGAATTCTTGTTAAAATAAAATTCAATGGTAAA
*
1324644 ATAAAATAAAAGTAAAGTCCAAATAAACTAGACTTCTTTTATTTTATTTCAATTAGAATAGGTCA
196 ATAAAATAAAAGTAAAGTCCAAATAAACTAGACTTCTTTTATTTTATTTCAATTAAAATAGGTCA
* *
1324709 TCTATTTTATTTTAATTAGAATAAGGTGTTTCAATCTTACTACGTTACTTCTATTAGTTATTGAT
261 TCTATTTTATTTTAATTAGAATAAGGTGTTTCAACCTTACTACATTACTTCTATTAGTTATTGAT
* * * *
1324774 TGGAATAAGATTTTTCAACCTATAAATAGGCATAGTCATCTCCTCTTGTAGGCATA
326 TGAAATAAGATATTTCAACCTATAAATAGACATAGTCATATCCTCTTGTAGGCATA
*
1324830 GTCCTCATCTGGCCAAGCCTCATTACATGACTTTATCCCATCAAGTTAAGCTTTGTTGATGGTAT
1 GTCCTCATCTGGCCAACCCTCATTACATGACTTTATCCCATCAAGTTAAGCTTTGTTGATGGTAT
* * * *
1324895 TAAGGTCCAAATCATCCCAATCGTTAGGACTTTTCTCTTGTTAGAATTGGGTGACTAGAATTTTT
66 TAAAGTCCAAATCATCCCAATCGTTAGGACTTTTCTCCTATTAGAATTGGGTGACTAGAATTCTT
* * *
1324960 GTTAAGGTGGAGATTGTTAGAATTGGGTGACTAGAATTCTTGTTAAAATAAAATTCAGTGGTAAA
131 ATTAAGGTGGAGATTATTAGAATTGGGTGACTAGAATTCTTGTTAAAATAAAATTCAATGGTAAA
* *
1325025 ATAAAATAAAAGTAGAGTCCAAATAAACTAGACTTCTTTTATTTTATTTTAATTAAAATAGGTCA
196 ATAAAATAAAAGTAAAGTCCAAATAAACTAGACTTCTTTTATTTTATTTCAATTAAAATAGGTCA
*
1325090 TCTATTTTATTTTAATTAGAATAAGGTGTTTCAACCTTACTACATTACTTCTATTAGTTGTTGAT
261 TCTATTTTATTTTAATTAGAATAAGGTGTTTCAACCTTACTACATTACTTCTATTAGTTATTGAT
* *
1325155 TGAAATAAGGTATTTCAACCTATAAATAGACATAGTCATATTCTCTTGTA
326 TGAAATAAGATATTTCAACCTATAAATAGACATAGTCATATCCTCTTGTA
1325205 ATTATTCAAT
Statistics
Matches: 352, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
381 352 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (381 bp):
GTCCTCATCTGGCCAACCCTCATTACATGACTTTATCCCATCAAGTTAAGCTTTGTTGATGGTAT
TAAAGTCCAAATCATCCCAATCGTTAGGACTTTTCTCCTATTAGAATTGGGTGACTAGAATTCTT
ATTAAGGTGGAGATTATTAGAATTGGGTGACTAGAATTCTTGTTAAAATAAAATTCAATGGTAAA
ATAAAATAAAAGTAAAGTCCAAATAAACTAGACTTCTTTTATTTTATTTCAATTAAAATAGGTCA
TCTATTTTATTTTAATTAGAATAAGGTGTTTCAACCTTACTACATTACTTCTATTAGTTATTGAT
TGAAATAAGATATTTCAACCTATAAATAGACATAGTCATATCCTCTTGTAGGCATA
Found at i:1328056 original size:17 final size:17
Alignment explanation
Indices: 1328034--1328072 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1328024 AGGTGGAGAA
* *
1328034 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
1328051 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
1328068 CTTGT
1 CTTGT
1328073 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:1328131 original size:41 final size:41
Alignment explanation
Indices: 1328074--1328157 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
1328064 AATTCTTGTC
1328074 AAGGTGGAGATTGTTAGAATTGGGTGACTAGAACTCTTATT
1 AAGGTGGAGATTGTTAGAATTGGGTGACTAGAACTCTTATT
* * *
1328115 AAGGTGGGGATTGTTAGAATTGGGTGACTAGAATTCTTGTT
1 AAGGTGGAGATTGTTAGAATTGGGTGACTAGAACTCTTATT
1328156 AA
1 AA
1328158 AATAAAATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.06, G:0.31, T:0.35
Consensus pattern (41 bp):
AAGGTGGAGATTGTTAGAATTGGGTGACTAGAACTCTTATT
Found at i:1329627 original size:2 final size:2
Alignment explanation
Indices: 1329620--1329645 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1329610 AAATTCAAAT
1329620 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1329646 CTAAACAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1335100 original size:21 final size:21
Alignment explanation
Indices: 1335076--1335116 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1335066 TTTATTTATT
1335076 TAAAT-TTAATTGTAAAATATA
1 TAAATATTAATT-TAAAATATA
*
1335097 TAAATATTAATTTATAATAT
1 TAAATATTAATTTAAAATAT
1335117 TTTTTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAATATTAATTTAAAATATA
Found at i:1338008 original size:4 final size:4
Alignment explanation
Indices: 1338001--1338062 Score: 52
Period size: 4 Copynumber: 14.8 Consensus size: 4
1337991 TGAGAGATAA
* * * *
1338001 AAAT AAAT AAAT AACT AAACA AAAT AAAT AAAGA AAAT AAAC AAAT GAAAT
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAA-T AAAT AAAT AAAT -AAAT
*
1338052 AAAT CAAT AAA
1 AAAT AAAT AAA
1338063 CCAATCAAGA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
4 35 0.78
5 10 0.22
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:1338024 original size:21 final size:20
Alignment explanation
Indices: 1338000--1338063 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
1337990 TTGAGAGATA
1338000 AAAATAAATAAATAACTAAAC
1 AAAATAAATAAATAA-TAAAC
*
1338021 AAAATAAATAAAGAAAATAAAC
1 AAAATAAAT-AA-ATAATAAAC
1338043 -AAATGAAATAAATCAATAAAC
1 AAAAT-AAATAAAT-AATAAAC
1338064 CAATCAAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 1 0.03
21 22 0.59
22 11 0.30
23 3 0.08
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.17
Consensus pattern (20 bp):
AAAATAAATAAATAATAAAC
Found at i:1340865 original size:18 final size:18
Alignment explanation
Indices: 1340842--1340884 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1340832 GAATAGGTTT
1340842 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
1340860 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
1340878 TTAATTA
1 TTAATTA
1340885 CACCTTGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Done.