Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001582.1 Hibiscus syriacus cultivar Beakdansim tig00003151_pilon, 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: 1162828
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1069219 original size:42 final size:42
Alignment explanation
Indices: 1069152--1069231 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
1069142 ACTTAGTAAG
*
1069152 TCCTTCGGGTCATCAGTAAGCCTTTCAAGCATGATGATTGAA
1 TCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGATTGAA
* * * *
1069194 TCCTTCGGGTCATCTGTCAGGCTTTCGAGCAAGATGAT
1 TCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGAT
1069232 AAGTTCTTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (42 bp):
TCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGATTGAA
Found at i:1079154 original size:18 final size:20
Alignment explanation
Indices: 1079126--1079162 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1079116 GTGTATTCCC
1079126 TTTTAAAATTAAA-TAAATG
1 TTTTAAAATTAAATTAAATG
1079145 TTTT-AAATTAAATTAAAT
1 TTTTAAAATTAAATTAAAT
1079163 TAAATTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTTTAAAATTAAATTAAATG
Found at i:1079738 original size:24 final size:24
Alignment explanation
Indices: 1079706--1079805 Score: 110
Period size: 24 Copynumber: 4.2 Consensus size: 24
1079696 TGTTCGGTAA
* *
1079706 TATGTTCGTTTAAGTTTGTTCATT
1 TATGTTCGTTTATGTTCGTTCATT
* *
1079730 TATGTTCGTTTGTGTTCATTCATT
1 TATGTTCGTTTATGTTCGTTCATT
* *
1079754 TATGTTCGTTTATGTTCGATCGTT
1 TATGTTCGTTTATGTTCGTTCATT
* ** *
1079778 TATGTTCATTTATGAGCATTCATT
1 TATGTTCGTTTATGTTCGTTCATT
1079802 TATG
1 TATG
1079806 CTTAGACCAA
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (24 bp):
TATGTTCGTTTATGTTCGTTCATT
Found at i:1079780 original size:48 final size:48
Alignment explanation
Indices: 1079706--1079805 Score: 128
Period size: 48 Copynumber: 2.1 Consensus size: 48
1079696 TGTTCGGTAA
* * * * **
1079706 TATGTTCGTTTAAGTTTGTTCATTTATGTTCGTTTGTGTTCATTCATT
1 TATGTTCGTTTAAGTTCGATCATTTATGTTCATTTATGAGCATTCATT
* *
1079754 TATGTTCGTTTATGTTCGATCGTTTATGTTCATTTATGAGCATTCATT
1 TATGTTCGTTTAAGTTCGATCATTTATGTTCATTTATGAGCATTCATT
1079802 TATG
1 TATG
1079806 CTTAGACCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (48 bp):
TATGTTCGTTTAAGTTCGATCATTTATGTTCATTTATGAGCATTCATT
Found at i:1080025 original size:10 final size:10
Alignment explanation
Indices: 1079970--1080008 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1079960 AAAATCTATT
1079970 TTCATTTATG
1 TTCATTTATG
* *
1079980 TTCCTTTACG
1 TTCATTTATG
*
1079990 TTCGTTTATG
1 TTCATTTATG
1080000 TTCATTTAT
1 TTCATTTAT
1080009 TGTGTTCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:1080283 original size:110 final size:110
Alignment explanation
Indices: 1080090--1080325 Score: 445
Period size: 110 Copynumber: 2.1 Consensus size: 110
1080080 CGTTTATCAT
* * *
1080090 TTAAATGAACAAACATAAATGAACACGAACAAGCTACATTCCTTAACGAACGAGCACGAACAAGA
1 TTAAACGAACGAACATAAATGAACAAGAACAAGCTACATTCCTTAACGAACGAGCACGAACAAGA
1080155 ATTTTTTTCGTTTATGTTCGTATTCGTTCATTTGTTCGGTTAATG
66 ATTTTTTTCGTTTATGTTCGTATTCGTTCATTTGTTCGGTTAATG
1080200 TTAAACGAACGAACATAAATGAACAAGAACAAGCTACATTCCTTAACGAACGAGCACGAACAAGA
1 TTAAACGAACGAACATAAATGAACAAGAACAAGCTACATTCCTTAACGAACGAGCACGAACAAGA
1080265 ATTTTTTTCGTTTATGTTCGTATTCGTTCATTTGTTCGGTTAATG
66 ATTTTTTTCGTTTATGTTCGTATTCGTTCATTTGTTCGGTTAATG
1080310 TTAAACGAACGAACAT
1 TTAAACGAACGAACAT
1080326 GAACATACCT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 123 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (110 bp):
TTAAACGAACGAACATAAATGAACAAGAACAAGCTACATTCCTTAACGAACGAGCACGAACAAGA
ATTTTTTTCGTTTATGTTCGTATTCGTTCATTTGTTCGGTTAATG
Found at i:1082110 original size:16 final size:16
Alignment explanation
Indices: 1082089--1082122 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1082079 TTTCAGTGAA
* *
1082089 ATATGTATATATATAT
1 ATATGTAAACATATAT
1082105 ATATGTAAACATATAT
1 ATATGTAAACATATAT
1082121 AT
1 AT
1082123 TTATCAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (16 bp):
ATATGTAAACATATAT
Found at i:1082851 original size:29 final size:29
Alignment explanation
Indices: 1082795--1083015 Score: 259
Period size: 29 Copynumber: 7.6 Consensus size: 29
1082785 ACACCCTAAC
* * *
1082795 AAAAATTAATTACAAAACTAACATCTTTTT
1 AAAAA-TAATTACAAAAATAGCACCTTTTT
* * *
1082825 AAAAATATTTACGAAATTAGCACCTTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTT
* *
1082854 AAAAATAATTACAAAAATAGTACATTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTT
* *
1082883 AAAAATAATTATAAAAATAACACCTTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTT
* *
1082912 -AAAATATTTACAAAAATATCA-CTGTTTT
1 AAAAATAATTACAAAAATAGCACCT-TTTT
*
1082940 AAAAATAATTACAAAAATAGCACATTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTT
* *
1082969 AAAAATATTTACAAAAATATCA-CTATTTT
1 AAAAATAATTACAAAAATAGCACCT-TTTT
1082998 AAAAATAATTACAAAAAT
1 AAAAATAATTACAAAAAT
1083016 GTCACCGGGT
Statistics
Matches: 163, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
27 2 0.01
28 23 0.14
29 132 0.81
30 6 0.04
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAAATAATTACAAAAATAGCACCTTTTT
Found at i:1091857 original size:2 final size:2
Alignment explanation
Indices: 1091795--1091844 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1091785 ATACCTTATT
1091795 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
1091837 TA TA TA TA
1 TA TA TA TA
1091845 CATGTGCATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1106389 original size:164 final size:165
Alignment explanation
Indices: 1106209--1106536 Score: 622
Period size: 164 Copynumber: 2.0 Consensus size: 165
1106199 GTCGTATTCA
*
1106209 AATTTCCCCCTATTATTTTCATCATTTCCCGCTTTTTCTTCCTCGATAATTATCAGTTCACGCCG
1 AATTTCCCCCTATTATTTTCATCATTTCCCGCTTTTTCTCCCTCGATAATTATCAGTTCACGCCG
1106274 CTTCTTCCACTTTTTCTCTTTTTCCA-TTTTCCCTTTCTCCAAAACGACATCTTCTCCAACAATA
66 CTTCTTCCACTTTTTCTCTTTTTCCATTTTTCCCTTTCTCCAAAACGACATCTTCTCCAACAATA
*
1106338 TCGTTATGTTCTCTAAATCGTATTGCCCGTATGCT
131 TCGTTATGTTCTCTAAATCGTATTACCCGTATGCT
*
1106373 AATTTCCCCCTATTATTTTCATCATTTCCCGCTTTTTCTCCCTCGATAATTATTAGTTCACGCCG
1 AATTTCCCCCTATTATTTTCATCATTTCCCGCTTTTTCTCCCTCGATAATTATCAGTTCACGCCG
1106438 CTTCTTCCACTTTTTCTCTTTTTCCATTTTTCCCTTTCTCCAAAACGACATCTTCTCCAACAATA
66 CTTCTTCCACTTTTTCTCTTTTTCCATTTTTCCCTTTCTCCAAAACGACATCTTCTCCAACAATA
1106503 TCGTTATGTTCTCTAAATCGTATTACCCGTATGC
131 TCGTTATGTTCTCTAAATCGTATTACCCGTATGC
1106537 CATTTTTCTC
Statistics
Matches: 160, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
164 89 0.56
165 71 0.44
ACGTcount: A:0.19, C:0.30, G:0.07, T:0.43
Consensus pattern (165 bp):
AATTTCCCCCTATTATTTTCATCATTTCCCGCTTTTTCTCCCTCGATAATTATCAGTTCACGCCG
CTTCTTCCACTTTTTCTCTTTTTCCATTTTTCCCTTTCTCCAAAACGACATCTTCTCCAACAATA
TCGTTATGTTCTCTAAATCGTATTACCCGTATGCT
Found at i:1106469 original size:16 final size:17
Alignment explanation
Indices: 1106442--1106479 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1106432 ACGCCGCTTC
*
1106442 TTCCACTTTTTCTCTTT
1 TTCCACTTTTTCCCTTT
1106459 TTCCA-TTTTTCCCTTT
1 TTCCACTTTTTCCCTTT
*
1106475 CTCCA
1 TTCCA
1106480 AAACGACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.08, C:0.34, G:0.00, T:0.58
Consensus pattern (17 bp):
TTCCACTTTTTCCCTTT
Found at i:1107187 original size:16 final size:16
Alignment explanation
Indices: 1107166--1107202 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1107156 GATGGTATAA
1107166 TGCAAAGGTTTCTAAC
1 TGCAAAGGTTTCTAAC
*
1107182 TGCAAAGGTTTCTAGC
1 TGCAAAGGTTTCTAAC
1107198 TGCAA
1 TGCAA
1107203 GTTGATGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (16 bp):
TGCAAAGGTTTCTAAC
Found at i:1110153 original size:2 final size:2
Alignment explanation
Indices: 1110146--1110172 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1110136 TCAATCTACA
1110146 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1110173 ATTTACGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1110280 original size:13 final size:13
Alignment explanation
Indices: 1110259--1110310 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
1110249 AATGACGCGC
*
1110259 AATGAGCGTCATA
1 AATGCGCGTCATA
1110272 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
1110285 AATGTGTGTCATA
1 AATGCGCGTCATA
* *
1110298 AAGGCGTGTCATA
1 AATGCGCGTCATA
1110311 GATTTATGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:1110288 original size:26 final size:26
Alignment explanation
Indices: 1110259--1110310 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1110249 AATGACGCGC
*
1110259 AATGAGCGTCATAAATGCGCGTCATA
1 AATGAGCGTCATAAAGGCGCGTCATA
* * *
1110285 AATGTGTGTCATAAAGGCGTGTCATA
1 AATGAGCGTCATAAAGGCGCGTCATA
1110311 GATTTATGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (26 bp):
AATGAGCGTCATAAAGGCGCGTCATA
Found at i:1119182 original size:22 final size:22
Alignment explanation
Indices: 1119157--1119233 Score: 54
Period size: 22 Copynumber: 3.5 Consensus size: 22
1119147 CAGAGGAAAT
1119157 CGATCCCCCCTCATGAGGGAAC
1 CGATCCCCCCTCATGAGGGAAC
* *
1119179 CGAT-TCCCCT-TTGAAGGGGAAC
1 CGATCCCCCCTCATG-A-GGGAAC
* *
1119201 CGATTCCCCCTACA-G-GGGAAT
1 CGATCCCCCCT-CATGAGGGAAC
1119222 CGATACCCCCCT
1 CGAT-CCCCCCT
1119234 GGGGTTCTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 2 0.05
21 15 0.35
22 20 0.47
23 5 0.12
24 1 0.02
ACGTcount: A:0.22, C:0.38, G:0.22, T:0.18
Consensus pattern (22 bp):
CGATCCCCCCTCATGAGGGAAC
Found at i:1119219 original size:21 final size:21
Alignment explanation
Indices: 1119173--1119231 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1119163 CCCCTCATGA
*
1119173 GGGAACCGATTCCCCTTTGAAG
1 GGGAACCGATTCCCC-CTGAAG
1119195 GGGAACCGATTCCCCCT-ACAG
1 GGGAACCGATTCCCCCTGA-AG
* *
1119216 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
1119232 CTGGGGTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 17 0.52
22 15 0.45
ACGTcount: A:0.24, C:0.34, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTGAAG
Found at i:1126950 original size:53 final size:53
Alignment explanation
Indices: 1126873--1126997 Score: 207
Period size: 53 Copynumber: 2.4 Consensus size: 53
1126863 CTTGACACTA
*
1126873 TAAGAGC-TTCGAGAGATTGTCTGGTCCCTAGGCGAAACATTTCTAGACCTTG
1 TAAGAGCTTTCGAGAGATTGCCTGGTCCCTAGGCGAAACATTTCTAGACCTTG
* * *
1126925 TAAGAGCTTTCGAGAGATTGCCTGGTGCTTAGGTGAAACATTTCTAGACCTTG
1 TAAGAGCTTTCGAGAGATTGCCTGGTCCCTAGGCGAAACATTTCTAGACCTTG
1126978 TAAGAGCTTTCGAGAGATTG
1 TAAGAGCTTTCGAGAGATTG
1126998 TCGTTTTTCT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
52 7 0.10
53 61 0.90
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (53 bp):
TAAGAGCTTTCGAGAGATTGCCTGGTCCCTAGGCGAAACATTTCTAGACCTTG
Found at i:1129949 original size:13 final size:13
Alignment explanation
Indices: 1129933--1129970 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1129923 TGTTTCTGTT
1129933 TTTCTTTACTTTA
1 TTTCTTTACTTTA
1129946 TTTCTTTACTTTA
1 TTTCTTTACTTTA
1129959 TTTCTTTA-TTTA
1 TTTCTTTACTTTA
1129971 CTTTTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCTTTACTTTA
Found at i:1130969 original size:103 final size:101
Alignment explanation
Indices: 1130782--1130986 Score: 277
Period size: 103 Copynumber: 2.0 Consensus size: 101
1130772 TCACGGGATG
* * *
1130782 ACTCTACCTGACTAGCTCAGGGTGGACGGTATGCTCCCTTTCACTTAGAGTGTAGGATGGTAGTG
1 ACTCTACCTGACTAGCTCAGGGTGGAAGGTATGATCCCTTTCACTTAGAATGTAGGATGGTAGTG
* ** ** *
1130847 TGATGAGCTGATTGTCCTTATTGTGTGCTTTAAAAAA
66 TGATGAGCTGACTCCCCTTAAAGTATGC-TTAAAAAA
* *
1130884 ACTCTACCTGACTAG-TACGGAGGTGGAAGGTATGATCCCTTTCACTTAGAATGTGGGATGGTAG
1 ACTCTACCTGACTAGCT-CAG-GGTGGAAGGTATGATCCCTTTCACTTAGAATGTAGGATGGTAG
1130948 TGTGATGAGCTGACTCCCCTTAAAGTATGCTTAAAAAA
64 TGTGATGAGCTGACTCCCCTTAAAGTATGCTTAAAAAA
1130986 A
1 A
1130987 GTTGAAGTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
101 1 0.01
102 26 0.29
103 63 0.70
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (101 bp):
ACTCTACCTGACTAGCTCAGGGTGGAAGGTATGATCCCTTTCACTTAGAATGTAGGATGGTAGTG
TGATGAGCTGACTCCCCTTAAAGTATGCTTAAAAAA
Found at i:1132685 original size:323 final size:323
Alignment explanation
Indices: 1132097--1132742 Score: 1238
Period size: 323 Copynumber: 2.0 Consensus size: 323
1132087 ATGAATATTA
1132097 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
1 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
*
1132162 TTTTACCGGTAATGAATGATTAAGTATGTTTTTGATAAGTGTTGTTTTGTTCACTATTTTAACCT
66 TTTTACCGGTAATGAATGATTAAGTATGTTTTTGATAAGTGTTGTTTAGTTCACTATTTTAACCT
*
1132227 TTCGCCTTTACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
131 TTCGCCTTGACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
1132292 TGTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCGAGAGATTTAAGA
196 TGTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCGAGAGATTTAAGA
1132357 TAGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCTGCCTTAGAG
261 TAGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCTGCCTTAGAG
1132420 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
1 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
* * *
1132485 TTTTACCGTTAATGAATGATTAAGTATGTTTTTGTTAAGTGTTGTTTAGTTCACTGTTTTAACCT
66 TTTTACCGGTAATGAATGATTAAGTATGTTTTTGATAAGTGTTGTTTAGTTCACTATTTTAACCT
*
1132550 TTTGCCTTGACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
131 TTCGCCTTGACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
1132615 TGTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCGAGAGATTTAAGA
196 TGTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCGAGAGATTTAAGA
1132680 TAGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCTGCCTTAGAG
261 TAGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCTGCCTTAGAG
1132743 ATAAGGAGAG
Statistics
Matches: 317, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
323 317 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (323 bp):
TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
TTTTACCGGTAATGAATGATTAAGTATGTTTTTGATAAGTGTTGTTTAGTTCACTATTTTAACCT
TTCGCCTTGACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
TGTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCGAGAGATTTAAGA
TAGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCTGCCTTAGAG
Found at i:1135725 original size:5 final size:5
Alignment explanation
Indices: 1135715--1135739 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1135705 AAAGGATCCC
1135715 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
1135740 CGAACTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:1136186 original size:18 final size:19
Alignment explanation
Indices: 1136155--1136195 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
1136145 TTTCAGAATC
1136155 TTTTAATTCTAAAAATTAT
1 TTTTAATTCTAAAAATTAT
*
1136174 TTTTTATTC-AAAAATTAT
1 TTTTAATTCTAAAAATTAT
1136192 TTTT
1 TTTT
1136196 GAAAAAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAATTCTAAAAATTAT
Found at i:1139625 original size:112 final size:112
Alignment explanation
Indices: 1139428--1139817 Score: 546
Period size: 112 Copynumber: 3.5 Consensus size: 112
1139418 TTACTTTACA
* * *
1139428 ATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAACTCTTTACCGGTTTTATCATAATGAA
1 ATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGATTTTGTCATAATGAA
*
1139493 ACTGGTTTTTGTCATA-TTTTACTTGTTATATTGTAAAGAATCGATAC
66 ACTGG-TTTTGTCATATTTTTACATGTTATATTGTAAAGAATCGATAC
* * *
1139540 ATTTTTATAAAGTATCGATACTTTCAACATATCTGGTATCTCTTTACCGATTTTGTCATAATAAA
1 ATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGATTTTGTCATAATGAA
*
1139605 ACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCGATAC
66 ACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGAATCGATAC
*
1139652 A----T-T-AAGTATCGATACTTTCAACATATCCGGTAGCACTTTACC-AGTTTTGTCATAATGA
1 ATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGA-TTTTGTCATAATGA
* *
1139710 AATTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGAATCGATAA
65 AACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGAATCGATAC
* ** * *
1139758 ATGTACA-AGAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTGTCATA
1 ATTTTTATA-AAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGATTTTGTCATA
1139818 TTTTTACCTG
Statistics
Matches: 250, Mismatches: 18, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
105 1 0.00
106 95 0.38
107 1 0.00
108 1 0.00
111 10 0.04
112 142 0.57
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (112 bp):
ATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGATTTTGTCATAATGAA
ACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGAATCGATAC
Found at i:1140065 original size:74 final size:73
Alignment explanation
Indices: 1139953--1140192 Score: 351
Period size: 72 Copynumber: 3.3 Consensus size: 73
1139943 TTCAACATAT
* * *
1139953 CCGGTAAGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACTGTTTACATTATTAGCAACCT
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTA-TTTTTTTACCGTTTACATTATTAGCAACCT
1140018 TCAAAAAAA
65 TCAAAAAAA
*
1140027 CCGGTAGGTATTTTAATGTAATAGGTAGCG-CTATTTTTTTACCGTTTTCATTATTAGCAACCTT
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGCAACCTT
1140091 CAAAAAAA
66 CAAAAAAA
* * * * * *
1140099 -TGATATGTATTTTAATGTAATAGGTAGTGCCTATTTTTTTACCGTTTATATTATTAACAACCTT
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGCAACCTT
1140163 -AAAAAAA
66 CAAAAAAA
*
1140170 CCAGTAGGTATTTTAATGTAATA
1 CCGGTAGGTATTTTAATGTAATA
1140193 AATTTTGTTA
Statistics
Matches: 149, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
71 32 0.21
72 86 0.58
73 3 0.02
74 28 0.19
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (73 bp):
CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGCAACCTT
CAAAAAAA
Found at i:1140601 original size:158 final size:158
Alignment explanation
Indices: 1140311--1141104 Score: 1284
Period size: 158 Copynumber: 5.0 Consensus size: 158
1140301 ATAATACACA
* * * *
1140311 ACCTATTACGTTACATAAGCGCTACCAAATATGTTATTATACTTGATAATGTTTCCAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
* * * ** *
1140376 TCGATTATGTTATCATTGACAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAGGT
66 CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
1140441 AATTAACATATTTTATTATATAAGCGCT
131 AATTAACATATTTTATTATATAAGCGCT
* * * * * * *
1140469 ACCTATAACGTTATATAAGTGCTACCCAATATGTTATTATACTTTATAATGTTTCTAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
*
1140534 TCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
66 CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
*
1140599 AATTAACATATTTTATTATATAAGTGCT
131 AATTAACATATTTTATTATATAAGCGCT
* *
1140627 ACATATTACGTTATATAAGCGCTACTTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
*
1140692 CCGGTTATGTTATCCTTGGTAACATTTTAGACGTTTACCTAATATGTTGTAATAACAAATTAAGT
66 CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
1140757 AATTAACATATTTTATTATATAAGCGCT
131 AATTAACATATTTTATTATATAAGCGCT
*
1140785 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCTAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
*
1140850 CCGGTTATGTTATTCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
66 CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
** *
1140915 TTTTAACCTATTTTATTATATAAGCGCT
131 AATTAACATATTTTATTATATAAGCGCT
* *
1140943 ACCTATTACGTTATTTAAGCGCTACCTAATATGTTATTGTGCTTGATATTGTTTCCAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
* * *
1141008 CTGGTTGTGTTATCCTTGGTAACATTTTAGACGTTTACCTAATATGTTGTAATAACAAATT-AGT
66 CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
*
1141072 AATTAACCTATTTTATTATATAAGCGCT
131 AATTAACATATTTTATTATATAAGCGCT
1141100 ACCTA
1 ACCTA
1141105 ATATGTGCTT
Statistics
Matches: 595, Mismatches: 41, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
157 34 0.06
158 561 0.94
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (158 bp):
ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAA
CCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
AATTAACATATTTTATTATATAAGCGCT
Found at i:1140631 original size:23 final size:23
Alignment explanation
Indices: 1140604--1140651 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1140594 TAAGTAATTA
** *
1140604 ACATATTTTATTATATAAGTGCT
1 ACATATTACATTATATAAGCGCT
*
1140627 ACATATTACGTTATATAAGCGCT
1 ACATATTACATTATATAAGCGCT
1140650 AC
1 AC
1140652 TTAATATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (23 bp):
ACATATTACATTATATAAGCGCT
Found at i:1140662 original size:23 final size:23
Alignment explanation
Indices: 1140614--1140663 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1140604 ACATATTTTA
* *
1140614 TTATATAAGTGCTACATATTACG
1 TTATATAAGCGCTACATAATACG
* *
1140637 TTATATAAGCGCTACTTAATATG
1 TTATATAAGCGCTACATAATACG
1140660 TTAT
1 TTAT
1140664 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (23 bp):
TTATATAAGCGCTACATAATACG
Found at i:1140820 original size:23 final size:23
Alignment explanation
Indices: 1140772--1140821 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1140762 ACATATTTTA
*
1140772 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
1140795 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
1140818 TTAT
1 TTAT
1140822 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:1140946 original size:23 final size:23
Alignment explanation
Indices: 1140920--1140970 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1140910 TAAGTTTTTA
**
1140920 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
* *
1140943 ACCTATTACGTTATTTAAGCGCT
1 ACCTATTACATTATATAAGCGCT
1140966 ACCTA
1 ACCTA
1140971 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:1140978 original size:23 final size:23
Alignment explanation
Indices: 1140930--1140980 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1140920 ACCTATTTTA
* *
1140930 TTATATAAGCGCTACCTATTACG
1 TTATTTAAGCGCTACCTAATACG
*
1140953 TTATTTAAGCGCTACCTAATATG
1 TTATTTAAGCGCTACCTAATACG
1140976 TTATT
1 TTATT
1140981 GTGCTTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (23 bp):
TTATTTAAGCGCTACCTAATACG
Found at i:1141177 original size:128 final size:128
Alignment explanation
Indices: 1140980--1141232 Score: 418
Period size: 128 Copynumber: 2.0 Consensus size: 128
1140970 AATATGTTAT
* ** * *
1140980 TGTGCTTGATATTGTTTCCAGTAATTAACTGGTTGTGTTATCCTTGGTAACATTTTAGACGTTTA
1 TGTGCTTGATAATGTTTCCAGTAATTAACCAGTTATGTTATCCTCGGTAACATTTTAGACGTTTA
1141045 CCTAATATGTTGTAATAACAAATT-AGTAATTAACCTATTTTATTATATAAGCGCTACCTAATA
66 CCTAATA-GTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTAATA
* * *
1141108 TGTGCTTGATAATGTTTCCCGTAATTAACCAGTTATGTTATCCTCGGTAACATTTTAGGCGTTTT
1 TGTGCTTGATAATGTTTCCAGTAATTAACCAGTTATGTTATCCTCGGTAACATTTTAGACGTTTA
1141173 CCTAATAGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTA
66 CCTAATAGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTA
1141233 TTACATTATA
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
127 16 0.14
128 100 0.86
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (128 bp):
TGTGCTTGATAATGTTTCCAGTAATTAACCAGTTATGTTATCCTCGGTAACATTTTAGACGTTTA
CCTAATAGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTAATA
Found at i:1141231 original size:23 final size:23
Alignment explanation
Indices: 1141205--1141255 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
1141195 TAAGTAATTA
**
1141205 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
1141228 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
1141251 ACCTA
1 ACCTA
1141256 ATATGTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:1150839 original size:18 final size:18
Alignment explanation
Indices: 1150816--1150851 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1150806 TTCTTTAGAT
1150816 GATACTAAAGCTTAAAGA
1 GATACTAAAGCTTAAAGA
*
1150834 GATACTTAAGCTTAAAGA
1 GATACTAAAGCTTAAAGA
1150852 AAGCTTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (18 bp):
GATACTAAAGCTTAAAGA
Found at i:1152112 original size:21 final size:21
Alignment explanation
Indices: 1152082--1152121 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1152072 TTCTATATGG
1152082 TCCTTCGGAACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
1152103 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
1152122 GGTACCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:1152131 original size:21 final size:20
Alignment explanation
Indices: 1152079--1152154 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 20
1152069 GGATTCTATA
1152079 TGGTCCTTCGGAACATATATG
1 TGGTCCTT-GGAACATATATG
**
1152100 TAATCCTTTGGAACATATATG
1 TGGTCC-TTGGAACATATATG
* *
1152121 TGGTACCTTGGTACACT-TATT
1 TGGT-CCTTGGAACA-TATATG
1152142 TGGTCCATTGGAA
1 TGGTCC-TTGGAA
1152155 TATGTATATG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
20 2 0.05
21 37 0.84
22 5 0.11
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (20 bp):
TGGTCCTTGGAACATATATG
Done.