Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002875.1 Hibiscus syriacus cultivar Beakdansim tig00005929_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: 1473696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1232543 original size:20 final size:23
Alignment explanation
Indices: 1232500--1232543 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1232490 TCTTTCCATT
1232500 AAATACATATTTTTATTGAATAA
1 AAATACATATTTTTATTGAATAA
1232523 AAATAC-TATTTTT-TT-AATAA
1 AAATACATATTTTTATTGAATAA
1232543 A
1 A
1232544 TGTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 7 0.33
23 6 0.29
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATACATATTTTTATTGAATAA
Found at i:1234451 original size:33 final size:33
Alignment explanation
Indices: 1234409--1234618 Score: 269
Period size: 33 Copynumber: 6.3 Consensus size: 33
1234399 ATGAGAAGTA
*
1234409 GTGAATCCTTCAGCATTGATGCATATATTAATT
1 GTGAATCCTTCAGCATTGATGCATATATTAGTT
* **
1234442 GTGAATCCTTCAGAATCAATGCATATATTAGTT
1 GTGAATCCTTCAGCATTGATGCATATATTAGTT
* * *
1234475 GTGACTCTTTCAGCATTGGTGCATATATTAGTT
1 GTGAATCCTTCAGCATTGATGCATATATTAGTT
* *
1234508 GTGAATCCTTCAACATTGGTGCATATATTAGTT
1 GTGAATCCTTCAGCATTGATGCATATATTAGTT
* *
1234541 GTGAATCCTTCAGCA-TCAGTGCATATATATTAGTC
1 GTGAATCCTTCAGCATTGA-TGC--ATATATTAGTT
* *
1234576 GTGAATCCTTCAGCATTGGTGTATATATTAGTT
1 GTGAATCCTTCAGCATTGATGCATATATTAGTT
1234609 GTGAATCCTT
1 GTGAATCCTT
1234619 TGAAACTTAA
Statistics
Matches: 152, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 123 0.81
35 27 0.18
36 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (33 bp):
GTGAATCCTTCAGCATTGATGCATATATTAGTT
Found at i:1234601 original size:99 final size:98
Alignment explanation
Indices: 1234409--1234618 Score: 312
Period size: 99 Copynumber: 2.1 Consensus size: 98
1234399 ATGAGAAGTA
*
1234409 GTGAATCCTTCAGCATTGATGCATATATTAATTGTGAATCCTTCAGAATCAATGCATATATTAGT
1 GTGAATCCTTCAACATTGATGCATATATTAATTGTGAATCCTTCAGAATCAATGCATATATTAGT
* * *
1234474 TGTGACTCTTTCAGCATTGGTGCATATATTAGTT
66 CGTGAATCCTTCAGCATTGGTG-ATATATTAGTT
* * * *
1234508 GTGAATCCTTCAACATTGGTGCATATATTAGTTGTGAATCCTTCAGCATCAGTGCATATATATTA
1 GTGAATCCTTCAACATTGATGCATATATTAATTGTGAATCCTTCAGAATCAATGC--ATATATTA
1234573 GTCGTGAATCCTTCAGCATTGGTGTATATATTAGTT
64 GTCGTGAATCCTTCAGCATTGGTG-ATATATTAGTT
1234609 GTGAATCCTT
1 GTGAATCCTT
1234619 TGAAACTTAA
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 50 0.50
101 50 0.50
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (98 bp):
GTGAATCCTTCAACATTGATGCATATATTAATTGTGAATCCTTCAGAATCAATGCATATATTAGT
CGTGAATCCTTCAGCATTGGTGATATATTAGTT
Found at i:1237310 original size:19 final size:20
Alignment explanation
Indices: 1237283--1237322 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1237273 AATATATATA
* *
1237283 TATATATAATATTAATATTT
1 TATATATAAAAATAATATTT
1237303 TATA-ATAAAAATAATATTT
1 TATATATAAAAATAATATTT
1237322 T
1 T
1237323 TCTCTGTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATATAAAAATAATATTT
Found at i:1248085 original size:2 final size:2
Alignment explanation
Indices: 1248078--1248110 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1248068 TTTGCACAGG
1248078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1248111 CCTTCGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1249942 original size:42 final size:40
Alignment explanation
Indices: 1249912--1250165 Score: 230
Period size: 42 Copynumber: 6.2 Consensus size: 40
1249902 TTCGCGTAGT
* *
1249912 GATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGATTTTCCAAGTTCGTTGC
* *
1249952 GATAGTCCAAGTT--CGTTGCGATAGTT-GAAGTTCGCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGAT-TTTCCAAGTT--CGTTGC
* * **
1249992 GATTTATTCCAAATT--CGTTGCGATAGTCCAAGTTCGTTGC
1 GA--TAGTCCAAGTTCGCGTTGCGATTTTCCAAGTTCGTTGC
* * * * *
1250032 GATAGTCGAAGTTCGCGTTGCGATTTATTTTCAAATTCGCTAC
1 GATAGTCCAAGTTCGCGTTGCGA--T-TTTCCAAGTTCGTTGC
1250075 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAGTTCGTTGC
* *
1250117 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAGTTCGTTGC
1250159 GATAGTC
1 GATAGTC
1250166 TAAAATCGCA
Statistics
Matches: 177, Mismatches: 25, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
38 21 0.12
39 2 0.01
40 36 0.20
41 2 0.01
42 84 0.47
43 32 0.18
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (40 bp):
GATAGTCCAAGTTCGCGTTGCGATTTTCCAAGTTCGTTGC
Found at i:1249951 original size:19 final size:19
Alignment explanation
Indices: 1249927--1250162 Score: 159
Period size: 19 Copynumber: 11.5 Consensus size: 19
1249917 TCGAAGTTCG
* *
1249927 CGTTGCGATTTTCCAAATT
1 CGTTGCGATATTCCAAGTT
*
1249946 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATATTCCAAGTT
*
1249965 CGTTGCGATAGTT-GAAGTT
1 CGTTGCGATA-TTCCAAGTT
*
1249984 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA--TATTCCAAGTT
*
1250007 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATATTCCAAGTT
* *
1250026 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATATTCCAAGTT
* *
1250045 CGCGTTGCGATTTATTTTCAAATT
1 --CGTTGCGA--TA-TTCCAAGTT
* * *
1250069 CGCTACGATAGTCCAAGTT
1 CGTTGCGATATTCCAAGTT
1250088 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGA--TATTCCAAGTT
* *
1250111 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATATTCCAAGTT
*
1250130 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA--TATTCCAAGTT
1250153 CGTTGCGATA
1 CGTTGCGATA
1250163 GTCTAAAATC
Statistics
Matches: 171, Mismatches: 27, Indels: 38
0.72 0.11 0.16
Matches are distributed among these distances:
19 75 0.44
20 3 0.02
21 54 0.32
22 8 0.05
23 26 0.15
24 5 0.03
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (19 bp):
CGTTGCGATATTCCAAGTT
Found at i:1249961 original size:61 final size:60
Alignment explanation
Indices: 1249887--1250098 Score: 300
Period size: 61 Copynumber: 3.4 Consensus size: 60
1249877 CATATTCGCA
* *
1249887 TTGCGATAGTCCAAGTTCGCGTAGTGATAGTCGAAGTTCGCGTTGCGA-TTTTCCAAATTCG
1 TTGCGATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTTCCAAATTCG
*
1249948 TTGCGATAGTCCAAGTTCGTTGCGATAGTTGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTT-TTCCAAATTCG
*
1250009 TTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTTCAAATTCG
1 TTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTTCCAAATTCG
* *
1250071 CTACGATAGTCCAAGTTCGCGTTGCGAT
1 TTGCGATAGTCCAAGTT--CGTTGCGAT
1250099 TTATTCCAAG
Statistics
Matches: 138, Mismatches: 7, Indels: 9
0.90 0.05 0.06
Matches are distributed among these distances:
59 26 0.19
60 2 0.01
61 73 0.53
62 27 0.20
63 1 0.01
64 9 0.07
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (60 bp):
TTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTTCCAAATTCG
Found at i:1266787 original size:98 final size:98
Alignment explanation
Indices: 1266618--1266813 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
1266608 CAGGAAAGTG
1266618 GGCCTAATTCAGGCCTTGGAGGGATTCAGTTGACTGGTCTGGAGCAAGAAAACTGCCTAAACTCT
1 GGCCTAATTCAGGCCTTGGAGGGATTCAGTTGACTGGTCTGGAGCAAGAAAACTGCCTAAACTCT
1266683 ATGGGCCGTAGTCCTTTTTCATCAGATACAATT
66 ATGGGCCGTAGTCCTTTTTCATCAGATACAATT
1266716 GGCCTAATTCAGGCCTTGGAGGGATTCAGTTGACTGGTCTGGAGCAAGAAAACTGCCTAAACTCT
1 GGCCTAATTCAGGCCTTGGAGGGATTCAGTTGACTGGTCTGGAGCAAGAAAACTGCCTAAACTCT
1266781 ATGGGCCGTAGTCCTTTTTCATCAGATACAATT
66 ATGGGCCGTAGTCCTTTTTCATCAGATACAATT
1266814 AAGGACTCAG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (98 bp):
GGCCTAATTCAGGCCTTGGAGGGATTCAGTTGACTGGTCTGGAGCAAGAAAACTGCCTAAACTCT
ATGGGCCGTAGTCCTTTTTCATCAGATACAATT
Found at i:1267334 original size:62 final size:64
Alignment explanation
Indices: 1267236--1267365 Score: 246
Period size: 62 Copynumber: 2.1 Consensus size: 64
1267226 TCCTCATCAG
1267236 CTTTTCCTTTGTTGGTTTGAGGAAGCAATTGCTACATGGGAAATTAGTAAGATGCTGGGGATA-
1 CTTTTCCTTTGTTGGTTTGAGGAAGCAATTGCTACATGGGAAATTAGTAAGATGCTGGGGATAT
1267299 CTTTTCCTTTGTTGG-TTGAGGAAGCAATTGCTACATGGGAAATTAGTAAGATGCTGGGGATAT
1 CTTTTCCTTTGTTGGTTTGAGGAAGCAATTGCTACATGGGAAATTAGTAAGATGCTGGGGATAT
1267362 CTTT
1 CTTT
1267366 CAAGGAGGGG
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 47 0.71
63 19 0.29
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.36
Consensus pattern (64 bp):
CTTTTCCTTTGTTGGTTTGAGGAAGCAATTGCTACATGGGAAATTAGTAAGATGCTGGGGATAT
Found at i:1275008 original size:38 final size:38
Alignment explanation
Indices: 1274955--1275031 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 38
1274945 ATGTTTGGTT
1274955 CAACCGTGATCAAGTAGATCCTTTATAATATAGATAGC
1 CAACCGTGATCAAGTAGATCCTTTATAATATAGATAGC
1274993 CAACCGTGA-CAAAGTAGATCCTTTATAATATAGATAGC
1 CAACCGTGATC-AAGTAGATCCTTTATAATATAGATAGC
1275031 C
1 C
1275032 GTTTGGCCGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 1 0.03
38 37 0.97
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (38 bp):
CAACCGTGATCAAGTAGATCCTTTATAATATAGATAGC
Found at i:1278798 original size:2 final size:2
Alignment explanation
Indices: 1278791--1278858 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1278781 TTAAAACATA
1278791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1278833 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1278859 TCTACTCATG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1280954 original size:62 final size:61
Alignment explanation
Indices: 1280852--1280979 Score: 238
Period size: 62 Copynumber: 2.1 Consensus size: 61
1280842 AAGAAAATAA
1280852 GAGAGGAGAACGGTGGAGAAGAAGGTGTTGCAACTACTTTTTTTAAAGCTTTTAGGGTAGGT
1 GAGAGGAGAACGGTGGAGAAGAAGGTGTTGCAACTAC-TTTTTTAAAGCTTTTAGGGTAGGT
*
1280914 GAGAGGAGAACGGTGGAGAAGAAGGTGTTGCAACTGCTTTTTTAAAGCTTTTAGGGTAGGT
1 GAGAGGAGAACGGTGGAGAAGAAGGTGTTGCAACTACTTTTTTAAAGCTTTTAGGGTAGGT
1280975 GAGAG
1 GAGAG
1280980 TCTCTCCTCG
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
61 29 0.45
62 36 0.55
ACGTcount: A:0.29, C:0.08, G:0.36, T:0.27
Consensus pattern (61 bp):
GAGAGGAGAACGGTGGAGAAGAAGGTGTTGCAACTACTTTTTTAAAGCTTTTAGGGTAGGT
Found at i:1299173 original size:36 final size:36
Alignment explanation
Indices: 1299131--1299201 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
1299121 TCACATTATT
1299131 ATTTTGAATGATATTATTTAAGTTAAGTTATCATTA
1 ATTTTGAATGATATTATTTAAGTTAAGTTATCATTA
1299167 ATTTTGAATGATATTATTTAAGTTAAGTTATCATT
1 ATTTTGAATGATATTATTTAAGTTAAGTTATCATT
1299202 TTAGGTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (36 bp):
ATTTTGAATGATATTATTTAAGTTAAGTTATCATTA
Found at i:1304129 original size:17 final size:17
Alignment explanation
Indices: 1304107--1304147 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1304097 GCTGTCATCA
1304107 TCGTCGTTGTCTCGTCG
1 TCGTCGTTGTCTCGTCG
*
1304124 TCGTCGTTGTCTTGTCG
1 TCGTCGTTGTCTCGTCG
*
1304141 TCATCGT
1 TCGTCGT
1304148 CGTCGTCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.02, C:0.27, G:0.27, T:0.44
Consensus pattern (17 bp):
TCGTCGTTGTCTCGTCG
Found at i:1304141 original size:20 final size:20
Alignment explanation
Indices: 1304099--1304157 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
1304089 GACTCCTCGC
*
1304099 TGTCATCATCGTCGTTGTC-
1 TGTCGTCATCGTCGTTGTCT
*
1304118 --TCGTCGTCGTCGTTGTCT
1 TGTCGTCATCGTCGTTGTCT
*
1304136 TGTCGTCATCGTCGTCGTCT
1 TGTCGTCATCGTCGTTGTCT
1304156 TG
1 TG
1304158 AGCATGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 15 0.45
20 18 0.55
ACGTcount: A:0.05, C:0.27, G:0.25, T:0.42
Consensus pattern (20 bp):
TGTCGTCATCGTCGTTGTCT
Found at i:1304490 original size:18 final size:18
Alignment explanation
Indices: 1304467--1304514 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1304457 GCGGCGACGG
*
1304467 CATCATATATGGTTGCGA
1 CATCATAAATGGTTGCGA
1304485 CATCATAAATGGTTGCGA
1 CATCATAAATGGTTGCGA
*
1304503 TATCATAAATGG
1 CATCATAAATGG
1304515 ATACGGTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (18 bp):
CATCATAAATGGTTGCGA
Found at i:1306232 original size:18 final size:17
Alignment explanation
Indices: 1306200--1306240 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1306190 GAATTATATT
1306200 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
*
1306217 AGTAAAGTACTTAAATAA
1 AGTAAAATA-TTAAATAA
*
1306235 ATTAAA
1 AGTAAA
1306241 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:1308056 original size:25 final size:25
Alignment explanation
Indices: 1308023--1308075 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1308013 CGGCTGCCAT
1308023 CATCGTCGTCGAAAGATCGCTCACC
1 CATCGTCGTCGAAAGATCGCTCACC
1308048 CATCGTCGTCGAAAGATCGCTCACC
1 CATCGTCGTCGAAAGATCGCTCACC
1308073 CAT
1 CAT
1308076 AGTCATCGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.21
Consensus pattern (25 bp):
CATCGTCGTCGAAAGATCGCTCACC
Found at i:1310419 original size:20 final size:21
Alignment explanation
Indices: 1310374--1310419 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1310364 TTTGATGATG
*
1310374 TTTATATATGAAATGGTTTCA
1 TTTATATATGAAATGATTTCA
* *
1310395 TTTATATATTAAAT-ATTTTA
1 TTTATATATGAAATGATTTCA
1310415 TTTAT
1 TTTAT
1310420 GTTATTATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTATATATGAAATGATTTCA
Found at i:1312212 original size:14 final size:14
Alignment explanation
Indices: 1312193--1312223 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1312183 TCCATTCCTC
*
1312193 AAACAAGAAAAATG
1 AAACAAGAAAAACG
1312207 AAACAAGAAAAACG
1 AAACAAGAAAAACG
1312221 AAA
1 AAA
1312224 TGCGAAATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.10, G:0.13, T:0.03
Consensus pattern (14 bp):
AAACAAGAAAAACG
Found at i:1316006 original size:11 final size:11
Alignment explanation
Indices: 1315990--1316038 Score: 71
Period size: 11 Copynumber: 4.5 Consensus size: 11
1315980 TTACAAATAT
1315990 AAAATTATAAA
1 AAAATTATAAA
1316001 AAAATTATAAA
1 AAAATTATAAA
* **
1316012 AAAAATCCAAA
1 AAAATTATAAA
1316023 AAAATTATAAA
1 AAAATTATAAA
1316034 AAAAT
1 AAAAT
1316039 CCACATCGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:1316023 original size:22 final size:21
Alignment explanation
Indices: 1315998--1316041 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 21
1315988 ATAAAATTAT
1315998 AAAAAAATTATAAAAAAAATCC
1 AAAAAAATTAT-AAAAAAATCC
1316020 AAAAAAATTATAAAAAAATCC
1 AAAAAAATTATAAAAAAATCC
1316041 A
1 A
1316042 CATCGTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAAAAATTATAAAAAAATCC
Found at i:1325134 original size:145 final size:145
Alignment explanation
Indices: 1324869--1325165 Score: 486
Period size: 145 Copynumber: 2.0 Consensus size: 145
1324859 GAAAGTTTCG
1324869 ACAAAATGGAAGTCGAATTCGGGCTCAAGGTATCAAAGCGAAATGGCTAATGAAATTTGGGACCG
1 ACAAAATGGAAGTCGAATTCGGGCTCAAGGTATCAAAGCGAAATGGCTAATGAAATTTGGGACCG
* ***
1324934 AAATGCCACCATCTAAGGCAATCGACGGTGGCTGACAGTGGCATCCAATTGCCTTCTATTTTTAT
66 AAAGGCCACCATCTAAGGCAATCGACGGTGGCTGACAGTGGCATCCAACCACCTTCTATTTTTAT
1324999 TTTATAGTTGGATGA
131 TTTATAGTTGGATGA
* * * *
1325014 ACAAAATGGAAGTCGAATTCGGGCTCAAGGTATCGAGGCGAAATTGCTAATGAAATTTGGGACTG
1 ACAAAATGGAAGTCGAATTCGGGCTCAAGGTATCAAAGCGAAATGGCTAATGAAATTTGGGACCG
* * * *
1325079 AAAGGCCATCATCTAAGGCAATCGACGGTGGTTGGCGGTGGCATCCAACCACCTTCTATTTTTAT
66 AAAGGCCACCATCTAAGGCAATCGACGGTGGCTGACAGTGGCATCCAACCACCTTCTATTTTTAT
1325144 TTTATAGTTGGATGA
131 TTTATAGTTGGATGA
1325159 ACAAAAT
1 ACAAAAT
1325166 AGGATAAAGA
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
145 140 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (145 bp):
ACAAAATGGAAGTCGAATTCGGGCTCAAGGTATCAAAGCGAAATGGCTAATGAAATTTGGGACCG
AAAGGCCACCATCTAAGGCAATCGACGGTGGCTGACAGTGGCATCCAACCACCTTCTATTTTTAT
TTTATAGTTGGATGA
Found at i:1333143 original size:9 final size:9
Alignment explanation
Indices: 1333139--1333207 Score: 68
Period size: 9 Copynumber: 7.7 Consensus size: 9
1333129 ATATTATAAA
*
1333139 TATTATTAT
1 TATTAATAT
*
1333148 TATTATTAT
1 TATTAATAT
*
1333157 TATAAATAT
1 TATTAATAT
*
1333166 TATTATTAT
1 TATTAATAT
*
1333175 TATTATTAT
1 TATTAATAT
*
1333184 TATTATTAT
1 TATTAATAT
1333193 TATTAA-AT
1 TATTAATAT
1333201 ATATTAA
1 -TATTAA
1333208 ATACATATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
8 2 0.04
9 52 0.96
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTAATAT
Found at i:1333147 original size:3 final size:3
Alignment explanation
Indices: 1333139--1333197 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
1333129 ATATTATAAA
* *
1333139 TAT TAT TAT TAT TAT TAT TAT AAA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1333187 TAT TAT TAT TA
1 TAT TAT TAT TA
1333198 AATATATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1333147 original size:12 final size:12
Alignment explanation
Indices: 1333130--1333206 Score: 84
Period size: 12 Copynumber: 6.4 Consensus size: 12
1333120 TTTTTACCCA
1333130 TATTATAAATAT
1 TATTATAAATAT
* *
1333142 TATTATTATTAT
1 TATTATAAATAT
1333154 TATTATAAATAT
1 TATTATAAATAT
* *
1333166 TATTATTATTAT
1 TATTATAAATAT
* *
1333178 TATTATTATTAT
1 TATTATAAATAT
1333190 TATTATTAAATA-
1 TATTA-TAAATAT
1333202 TATTA
1 TATTA
1333207 AATACATATA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
12 52 0.93
13 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATAAATAT
Found at i:1333208 original size:9 final size:10
Alignment explanation
Indices: 1333193--1333231 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
1333183 TTATTATTAT
1333193 TATTAAAT-A
1 TATTAAATAA
1333202 TATTAAATACA
1 TATTAAATA-A
1333213 TATATAAATAA
1 TAT-TAAATAA
1333224 TATTAAAT
1 TATTAAAT
1333232 TACAAGCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.30
10 5 0.19
11 8 0.30
12 6 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:1333338 original size:16 final size:16
Alignment explanation
Indices: 1333317--1333353 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1333307 CCTAATCCCT
*
1333317 AGCCGCCTCTGTCTCC
1 AGCCGCCTCTGCCTCC
1333333 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
1333349 A-CCGC
1 AGCCGC
1333354 TGCCACGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.08, C:0.54, G:0.19, T:0.19
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Found at i:1337706 original size:12 final size:12
Alignment explanation
Indices: 1337681--1337750 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
1337671 ACGAAGATAT
* *
1337681 CAGAAATCAAAA
1 CAGAATTCAGAA
1337693 CAGAATTCAGAA
1 CAGAATTCAGAA
1337705 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1337717 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1337729 CAGAAATCAGAA
1 CAGAATTCAGAA
1337741 CAGAATTCAG
1 CAGAATTCAG
1337751 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1337713 original size:24 final size:24
Alignment explanation
Indices: 1337679--1337787 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
1337669 TAACGAAGAT
*
1337679 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
1337703 AACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
1337727 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* ***
1337751 GTCATTTATCAGAACAGAATTCA-
1 ATCAGAAATCAGAACAGAATTCAG
*
1337774 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1337788 TAAAATATTT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1337750 original size:48 final size:47
Alignment explanation
Indices: 1337679--1337787 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
1337669 TAACGAAGAT
*
1337679 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
1337726 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
1337774 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1337788 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:1338931 original size:18 final size:18
Alignment explanation
Indices: 1338910--1338945 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1338900 CTTCCATCCG
*
1338910 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1338928 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1338946 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1339962 original size:3 final size:3
Alignment explanation
Indices: 1339954--1340001 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1339944 CCATTATATC
1339954 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1340002 CGGAAGCTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1342414 original size:12 final size:12
Alignment explanation
Indices: 1342389--1342458 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
1342379 ACGAAGATAT
* *
1342389 CAGAAATCAAAA
1 CAGAATTCAGAA
1342401 CAGAATTCAGAA
1 CAGAATTCAGAA
1342413 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1342425 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1342437 CAGAAATCAGAA
1 CAGAATTCAGAA
1342449 CAGAATTCAG
1 CAGAATTCAG
1342459 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1342421 original size:24 final size:24
Alignment explanation
Indices: 1342387--1342495 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
1342377 TAACGAAGAT
*
1342387 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
1342411 AACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
1342435 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* ***
1342459 GTCATTTATCAGAACAGAATTCA-
1 ATCAGAAATCAGAACAGAATTCAG
*
1342482 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1342496 TAAAATATTT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1342458 original size:48 final size:47
Alignment explanation
Indices: 1342387--1342495 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
1342377 TAACGAAGAT
*
1342387 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
1342434 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
1342482 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1342496 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:1343639 original size:18 final size:18
Alignment explanation
Indices: 1343618--1343653 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1343608 CTTCCATCCG
*
1343618 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1343636 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1343654 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1344966 original size:3 final size:3
Alignment explanation
Indices: 1344958--1345017 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
1344948 CCATTATATC
1344958 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1345006 ATA ATA ATA ATA
1 ATA ATA ATA ATA
1345018 CGGAAGCTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1355098 original size:11 final size:11
Alignment explanation
Indices: 1355082--1355133 Score: 81
Period size: 11 Copynumber: 4.9 Consensus size: 11
1355072 TGCTTGAAGA
1355082 GAAAAAAAAGT
1 GAAAAAAAAGT
1355093 GAAAAAAAAGT
1 GAAAAAAAAGT
1355104 GAAAAAAAA-T
1 GAAAAAAAAGT
1355114 GAAAAAAAAG-
1 GAAAAAAAAGT
*
1355124 AAAAAAAAAG
1 GAAAAAAAAG
1355134 AAGAAGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
10 19 0.49
11 20 0.51
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (11 bp):
GAAAAAAAAGT
Found at i:1355099 original size:10 final size:10
Alignment explanation
Indices: 1355084--1355130 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
1355074 CTTGAAGAGA
1355084 AAAAAAAGTG
1 AAAAAAAGTG
1355094 AAAAAAAAGTG
1 -AAAAAAAGTG
*
1355105 AAAAAAAATG
1 AAAAAAAGTG
*
1355115 AAAAAAA-AG
1 AAAAAAAGTG
1355124 AAAAAAA
1 AAAAAAA
1355131 AAGAAGAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 8 0.24
10 16 0.47
11 10 0.29
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (10 bp):
AAAAAAAGTG
Found at i:1355109 original size:21 final size:21
Alignment explanation
Indices: 1355078--1355133 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 21
1355068 ATTATGCTTG
1355078 AAGAGAAAAAAAAGTGAAAAAA
1 AAGA-AAAAAAAAGTGAAAAAA
*
1355100 AAGTGAAAAAAAA-TGAAAAAA
1 AAG-AAAAAAAAAGTGAAAAAA
1355121 AAGAAAAAAAAAG
1 AAGAAAAAAAAAG
1355134 AAGAAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 8 0.27
21 11 0.37
22 11 0.37
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (21 bp):
AAGAAAAAAAAAGTGAAAAAA
Found at i:1355144 original size:32 final size:32
Alignment explanation
Indices: 1355082--1355145 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1355072 TGCTTGAAGA
* *
1355082 GAAAAAAAAGTGAAAAAAAAGTGAAAAAAAAT
1 GAAAAAAAAGTAAAAAAAAAGAGAAAAAAAAT
1355114 GAAAAAAAAG-AAAAAAAAAGAAGAAGAAAAAA
1 GAAAAAAAAGTAAAAAAAAAG-AGAA-AAAAAA
1355146 AAGGGGGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 9 0.32
32 13 0.46
33 6 0.21
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (32 bp):
GAAAAAAAAGTAAAAAAAAAGAGAAAAAAAAT
Found at i:1357390 original size:113 final size:113
Alignment explanation
Indices: 1357192--1357632 Score: 697
Period size: 113 Copynumber: 3.9 Consensus size: 113
1357182 ATTCAAATCT
* * *
1357192 ATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1357257 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
1357305 ATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1357370 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
1357418 ATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* ** * * *
1357483 GAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTT-GCTCAAATCC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCT-GAATTC
* * * * * * *
1357531 ATCACTTGATGGAGCAGCTTCTCTAG-AGAAGTTCATAATTAGAAGAACTCATTTGAAGAAGGAA
1 ATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
1357595 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
1357633 GCATAATTCT
Statistics
Matches: 306, Mismatches: 21, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
112 70 0.23
113 236 0.77
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
ATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
Found at i:1357974 original size:3 final size:3
Alignment explanation
Indices: 1357961--1358006 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
1357951 ATATTATAAA
1357961 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1358007 AATATATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1358014 original size:9 final size:10
Alignment explanation
Indices: 1358002--1358040 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
1357992 TTATTATTAT
1358002 TATTAAAT-A
1 TATTAAATAA
1358011 TATTAAATACA
1 TATTAAATA-A
1358022 TATATAAATAA
1 TAT-TAAATAA
1358033 TATTAAAT
1 TATTAAAT
1358041 TACAAGCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.30
10 5 0.19
11 8 0.30
12 6 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:1358147 original size:16 final size:16
Alignment explanation
Indices: 1358126--1358162 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1358116 CCTAATCCCT
*
1358126 AGCCGCCTCTGTCTCC
1 AGCCGCCTCTGCCTCC
1358142 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
1358158 A-CCGC
1 AGCCGC
1358163 TGCCACGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.08, C:0.54, G:0.19, T:0.19
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Found at i:1364115 original size:2 final size:2
Alignment explanation
Indices: 1364064--1364099 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1364054 TCAGTCATGG
1364064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1364100 CTGTTTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1365837 original size:14 final size:14
Alignment explanation
Indices: 1365818--1365864 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
1365808 AGATTAAGTC
1365818 AATAATTATTTTAT
1 AATAATTATTTTAT
1365832 AATAATATAATTAATT-T
1 AATAAT-T-ATT--TTAT
1365849 AATAATTATTTTAT
1 AATAATTATTTTAT
1365863 AA
1 AA
1365865 CTTTTGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 4 0.14
16 4 0.14
17 7 0.25
18 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATAATTATTTTAT
Found at i:1368086 original size:2 final size:2
Alignment explanation
Indices: 1368075--1368113 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1368065 TTATCTAACC
1368075 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1368114 TCTTTCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1368682 original size:144 final size:146
Alignment explanation
Indices: 1368476--1368750 Score: 385
Period size: 144 Copynumber: 1.9 Consensus size: 146
1368466 AAATACTAAA
* * * *
1368476 TTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAATTACACATGTATTCTACTATGGTT
1 TTGAAAAATAAAAAATTTATTATCAAAAAGAGGAATTGAAAGTAAAAATGTATTCTACTATGGTT
* * * *
1368541 TAGGAGCACGTGGCTCAAATTTGGTAAAAAAAAGAGAATT-AAATAAATGATGAATTGAAGAAAT
66 TAGGAGAACGTGGCTCAAATATGGTAAAAAAAAG-GAATTAAAATAAAGGAGGAATTGAAGAAAT
1368605 AAGGAGATTATGAAAAT
130 AAGGAGATTATGAAAAT
*
1368622 TTGAAAAATAAAAAA-TTATTATCAAAAA-ATGAATTGAAAGTAAAAATGTATTCTACTATGGTT
1 TTGAAAAATAAAAAATTTATTATCAAAAAGAGGAATTGAAAGTAAAAATGTATTCTACTATGGTT
* * * * * *
1368685 TAGGATAATGTGGTTTAAATATGGTAAAAAAATGGAATTAAAATGAAGGAGGAATTGAAGAAATA
66 TAGGAGAACGTGGCTCAAATATGGTAAAAAAAAGGAATTAAAATAAAGGAGGAATTGAAGAAATA
1368750 A
131 A
1368751 TGAAATCATG
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
143 5 0.04
144 81 0.72
145 12 0.11
146 15 0.13
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (146 bp):
TTGAAAAATAAAAAATTTATTATCAAAAAGAGGAATTGAAAGTAAAAATGTATTCTACTATGGTT
TAGGAGAACGTGGCTCAAATATGGTAAAAAAAAGGAATTAAAATAAAGGAGGAATTGAAGAAATA
AGGAGATTATGAAAAT
Found at i:1368894 original size:14 final size:14
Alignment explanation
Indices: 1368875--1368901 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1368865 TCGAGTTGAC
1368875 TCGAATAACTCAAT
1 TCGAATAACTCAAT
1368889 TCGAATAACTCAA
1 TCGAATAACTCAA
1368902 AATTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (14 bp):
TCGAATAACTCAAT
Found at i:1374885 original size:60 final size:60
Alignment explanation
Indices: 1374772--1374889 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
1374762 GGAACAAAAT
* * * * *
1374772 TGATCATTTTGTTACTTTTAATAGTTGAGGGAATAATCAAATCGTCACTCTATAGTCAGA
1 TGATCATTTTGTAACTTTTAATAGTAGAAGGAATAATCAAATAGTCACCCTATAGTCAGA
* *
1374832 TGATCATTTTGTAACTTTTAATAGTAGAATGACTTAA-CAAAGTAGT-ACCCTATAGTCA
1 TGATCATTTTGTAACTTTTAATAGTAGAAGGA-ATAATCAAA-TAGTCACCCTATAGTCA
1374890 TGGGATCATT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
60 43 0.88
61 6 0.12
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (60 bp):
TGATCATTTTGTAACTTTTAATAGTAGAAGGAATAATCAAATAGTCACCCTATAGTCAGA
Found at i:1376347 original size:24 final size:24
Alignment explanation
Indices: 1376320--1376370 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
1376310 CAGTACAATT
1376320 TTTAAAAATGATA-ATAT-TATAATA
1 TTTAAAAAT-ATATATATATAT-ATA
*
1376344 TTTAAATATATATATATATATATA
1 TTTAAAAATATATATATATATATA
1376368 TTT
1 TTT
1376371 GGTAAAAGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.12
24 18 0.75
25 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTAAAAATATATATATATATATA
Found at i:1377683 original size:2 final size:2
Alignment explanation
Indices: 1377676--1377729 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1377666 AATAAAGGTA
1377676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1377718 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1377730 TCAGTTCAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1378457 original size:4 final size:4
Alignment explanation
Indices: 1378448--1378477 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1378438 TATGTTTCTC
1378448 TATT TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TA
1378478 ATTACGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1383211 original size:29 final size:29
Alignment explanation
Indices: 1383169--1383247 Score: 133
Period size: 29 Copynumber: 2.7 Consensus size: 29
1383159 CGGTGATCGG
1383169 TATATTTAC-CGATCTAACACCGGTCAGAT
1 TATATTT-CTCGATCTAACACCGGTCAGAT
*
1383198 TATATTTCTCGATCTAATACCGGTCAGAT
1 TATATTTCTCGATCTAACACCGGTCAGAT
1383227 TATATTTCTCGATCTAACACC
1 TATATTTCTCGATCTAACACC
1383248 TGTAGCAGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 1 0.02
29 46 0.98
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (29 bp):
TATATTTCTCGATCTAACACCGGTCAGAT
Found at i:1383383 original size:50 final size:48
Alignment explanation
Indices: 1383259--1383383 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 48
1383249 GTAGCAGTAA
*
1383259 AGCGCGCCCCTGAACCGCGCTATACACTGATTTGGCGCCACATGGGTAT
1 AGCGCGCCCCT-AACCGCGCTATACACTGATCTGGCGCCACATGGGTAT
* ** * **
1383308 AGTGCGCCCCCTGCCCAGCGATATACGGTGATCTGGCGCCACATGGGTAT
1 AGCGCG-CCCCTAACC-GCGCTATACACTGATCTGGCGCCACATGGGTAT
1383358 AGCGCGCACCCTAATCCGCGCTATAC
1 AGCGCGC-CCCTAA-CCGCGCTATAC
1383384 TTGGGTATCT
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
49 8 0.13
50 51 0.84
51 2 0.03
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.19
Consensus pattern (48 bp):
AGCGCGCCCCTAACCGCGCTATACACTGATCTGGCGCCACATGGGTAT
Found at i:1383521 original size:10 final size:10
Alignment explanation
Indices: 1383506--1383545 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1383496 TTTATAACAC
1383506 CAAATTCTCT
1 CAAATTCTCT
1383516 CAAATTCTCT
1 CAAATTCTCT
1383526 -AAATTTCTCT
1 CAAA-TTCTCT
*
1383536 CAAATACTCT
1 CAAATTCTCT
1383546 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1383865 original size:110 final size:111
Alignment explanation
Indices: 1383672--1383892 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 111
1383662 TGGAAATCAT
* *
1383672 ATATCTCTACACTTTACTGATACGGTAACATTTTAACGTTTCAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTCATACGGTAACATTTTAACGTTTCAATTTAATTTAAATTATTAGTAA
* *
1383737 TATTTAGTTGATTTATTTAATGCATGATTATTAG-TTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
* *
1383782 ATATCTCGACACTTTGCTCATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTCATACGGTAACATTTTAACGTTTCAATTTAATTTAAATTATTAGTAA
1383847 TAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
1383893 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 93 0.89
111 11 0.11
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTACTCATACGGTAACATTTTAACGTTTCAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
Found at i:1385426 original size:18 final size:18
Alignment explanation
Indices: 1385403--1385437 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1385393 ACAGCCACCA
1385403 CAGCCATATATGATGCCG
1 CAGCCATATATGATGCCG
1385421 CAGCCATATATGATGCC
1 CAGCCATATATGATGCC
1385438 ACCATCGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (18 bp):
CAGCCATATATGATGCCG
Found at i:1389575 original size:12 final size:12
Alignment explanation
Indices: 1389558--1389594 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1389548 ATTTATAAGA
1389558 GAGGAGAGATGC
1 GAGGAGAGATGC
1389570 GA-G-GAGATGC
1 GAGGAGAGATGC
1389580 GAGGAGAGATGC
1 GAGGAGAGATGC
1389592 GAG
1 GAG
1389595 AACCGGAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.39
11 2 0.09
12 12 0.52
ACGTcount: A:0.32, C:0.08, G:0.51, T:0.08
Consensus pattern (12 bp):
GAGGAGAGATGC
Found at i:1389842 original size:49 final size:51
Alignment explanation
Indices: 1389741--1389842 Score: 127
Period size: 49 Copynumber: 2.0 Consensus size: 51
1389731 CCCCTACGTG
* * *
1389741 GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCATGTGTAACCAAGTCA
1 GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGGAACCAAATCA
* * **
1389792 GCGTATAGCGCGGTGCA-GGGG-GCGCTATACTCCACGTGGCGCCAAATCA
1 GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGGAACCAAATCA
1389841 GC
1 GC
1389843 AAATAACGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 24 0.55
50 4 0.09
51 16 0.36
ACGTcount: A:0.22, C:0.28, G:0.34, T:0.16
Consensus pattern (51 bp):
GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGGAACCAAATCA
Found at i:1390695 original size:2 final size:2
Alignment explanation
Indices: 1390683--1390711 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1390673 TAAATATTTA
1390683 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1390712 TATTTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1396067 original size:27 final size:25
Alignment explanation
Indices: 1396026--1396075 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
1396016 GGAAAAGGTA
1396026 AGTTTAATTTCAGTTGGTTAATTCTTG
1 AGTTTAATTTCAGTT--TTAATTCTTG
1396053 AGTTTAAGTTT-AGTTTTAATTCT
1 AGTTTAA-TTTCAGTTTTAATTCT
1396076 AGGGGTGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.54
Consensus pattern (25 bp):
AGTTTAATTTCAGTTTTAATTCTTG
Found at i:1396673 original size:20 final size:22
Alignment explanation
Indices: 1396628--1396685 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1396618 GCATGGGTAG
1396628 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1396652 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1396672 TGCATCGATGCACT
1 TGCATCGATGCACT
1396686 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1397396 original size:25 final size:27
Alignment explanation
Indices: 1397355--1397406 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
1397345 GCTATGAGCT
*
1397355 TATATGAACATGTGAT-A-TGAAAATG
1 TATATGAACATGAGATAAGTGAAAATG
1397380 TATAGTGAA-ATGAGATAAGTGAAAATG
1 TATA-TGAACATGAGATAAGTGAAAATG
1397407 CCCATGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.43
26 5 0.22
27 8 0.35
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.29
Consensus pattern (27 bp):
TATATGAACATGAGATAAGTGAAAATG
Found at i:1399938 original size:21 final size:22
Alignment explanation
Indices: 1399880--1399939 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
1399870 CCGTGATCAG
* *
1399880 GGGGAATCGGTA-CCCCTTGGG
1 GGGGAATCTGTACCCCCTTGGA
*
1399901 GGGGAATCTGTTCCCCCTT-GA
1 GGGGAATCTGTACCCCCTTGGA
1399922 GGGGAATCTGTACCCCCT
1 GGGGAATCTGTACCCCCT
1399940 GGACATTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 28 0.82
22 6 0.18
ACGTcount: A:0.15, C:0.28, G:0.33, T:0.23
Consensus pattern (22 bp):
GGGGAATCTGTACCCCCTTGGA
Found at i:1401276 original size:20 final size:19
Alignment explanation
Indices: 1401239--1401285 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1401229 TTAAATCATT
*
1401239 TTTCAAAATTTCATTTTGGC
1 TTTCAAAATCTCATTTT-GC
*
1401259 TTTCAAAATCT-ATGTTTGT
1 TTTCAAAATCTCAT-TTTGC
1401278 TTTCAAAA
1 TTTCAAAA
1401286 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.49
Consensus pattern (19 bp):
TTTCAAAATCTCATTTTGC
Found at i:1402154 original size:226 final size:225
Alignment explanation
Indices: 1401755--1402202 Score: 855
Period size: 226 Copynumber: 2.0 Consensus size: 225
1401745 TGGAGGTTTG
1401755 CGGTTGGTAGGGAGTCTTCCATGTGGAACGAGCCGGAGGTGGAAGCCATCTTCTCGGTTGTAGGG
1 CGGTTGGTAGGGAGTCTTCCATGTGGAACGAGCCGGAGGTGGAAGCCATCTTCTCGGTTGTAGGG
1401820 AATTGGTAGAGCTTCTTCTAGGATCGTCTCAAGGTGGTTAAACATTCTTAACGAGTTAGGCTCTG
66 AATTGGTAGAGCTTCTTCTAGGATCGTCTCAAGGTGGTTAAACATTCTTAACGAGTTAGGCTCTG
1401885 ATGCCAATATTAGGATTATCAGAAGCTCGAATCGACAAACCGGAACGGTTTGCAAAGAGGGGTTG
131 ATGCCAATATTAGGATTATCAGAAGCTCGAATCGACAAACCGGAACGGTTTGCAAAGAGGGGTTG
1401950 GAAT-GTTTTGTGTTTAGGGAGTAAGGTGT
196 GAATGGTTTTGTGTTTAGGGAGTAAGGTGT
1401979 CGGTTGGTAGGGAGTCTTCCATGTGGAACGAGCCGGAGGTGGAAGCCATCTTCTCGGTTGTGTAG
1 CGGTTGGTAGGGAGTCTTCCATGTGGAACGAGCCGGAGGTGGAAGCCATCTTCTCGG-T-TGTAG
1402044 GGAATTGGTAGAGCTTCTTCTAGGATCGTCTCAAGGTGGTTAAACATTCTTAACGAGTTAGGCTC
64 GGAATTGGTAGAGCTTCTTCTAGGATCGTCTCAAGGTGGTTAAACATTCTTAACGAGTTAGGCTC
1402109 TGATGCCAATTATTAGGATTATCAGAAGCTCGAATCGAC-AACCGGAACGGTTTGCAAAGAGGGG
129 TGATGCCAA-TATTAGGATTATCAGAAGCTCGAATCGACAAACCGGAACGGTTTGCAAAGAGGGG
1402173 TTGGAATGGTTTTGTGTTTAGGGAGTAAGG
193 TTGGAATGGTTTTGTGTTTAGGGAGTAAGG
1402203 AGATTAAAAG
Statistics
Matches: 220, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
224 57 0.26
225 1 0.00
226 111 0.50
227 51 0.23
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (225 bp):
CGGTTGGTAGGGAGTCTTCCATGTGGAACGAGCCGGAGGTGGAAGCCATCTTCTCGGTTGTAGGG
AATTGGTAGAGCTTCTTCTAGGATCGTCTCAAGGTGGTTAAACATTCTTAACGAGTTAGGCTCTG
ATGCCAATATTAGGATTATCAGAAGCTCGAATCGACAAACCGGAACGGTTTGCAAAGAGGGGTTG
GAATGGTTTTGTGTTTAGGGAGTAAGGTGT
Found at i:1403621 original size:30 final size:29
Alignment explanation
Indices: 1403474--1403630 Score: 115
Period size: 29 Copynumber: 5.4 Consensus size: 29
1403464 ACCCGATGAC
* *
1403474 ATTTTGGGAATTATTTTGAAAAAGGTGAT
1 ATTTTGGTAATTATTTTTAAAAAGGTGAT
* * *
1403503 ATTTTGG-GATTTTTTTTAAAACA-GTGAC
1 ATTTTGGTAATTATTTTTAAAA-AGGTGAT
* * * *
1403531 ATTCTGCTAATTATTTTTAAAATA-ATGAC
1 ATTTTGGTAATTATTTTTAAAA-AGGTGAT
* * * * *
1403560 ATTTTGGGATTTA-TTTGATAAACGATGAT
1 ATTTTGGTAATTATTTTTA-AAAAGGTGAT
1403589 ATTTTGGTAATTATTTTTAATAAAGGTGAT
1 ATTTTGGTAATTATTTTTAA-AAAGGTGAT
*
1403619 ATTTTTGTAATT
1 ATTTTGGTAATT
1403631 TTTGAATGTG
Statistics
Matches: 99, Mismatches: 23, Indels: 11
0.74 0.17 0.08
Matches are distributed among these distances:
28 24 0.24
29 53 0.54
30 22 0.22
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (29 bp):
ATTTTGGTAATTATTTTTAAAAAGGTGAT
Found at i:1409969 original size:27 final size:26
Alignment explanation
Indices: 1409932--1409985 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 26
1409922 TCTCGGTCAC
1409932 ATCATCAGGTTGAAGAGGTAGAGCTG
1 ATCATCAGGTTGAAGAGGTAGAGCTG
1409958 ATCATTCAGGTTGAAGAGGTAGAGCTG
1 ATCA-TCAGGTTGAAGAGGTAGAGCTG
1409985 A
1 A
1409986 GACCTGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24
Consensus pattern (26 bp):
ATCATCAGGTTGAAGAGGTAGAGCTG
Found at i:1413296 original size:22 final size:21
Alignment explanation
Indices: 1413270--1413341 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
1413260 CGTTGATCAT
* *
1413270 GGGGAATCGGTACCCCCTTGGG
1 GGGGAATCTGTTCCCCC-TGGG
*
1413292 GGGGAATTTGTTCCCCCTGGG
1 GGGGAATCTGTTCCCCCTGGG
* *
1413313 GTGGAATTTGTTCCCCCT-GG
1 GGGGAATCTGTTCCCCCTGGG
1413333 GGGGAATCT
1 GGGGAATCT
1413342 ATACCCCTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.20
21 21 0.48
22 14 0.32
ACGTcount: A:0.12, C:0.24, G:0.38, T:0.26
Consensus pattern (21 bp):
GGGGAATCTGTTCCCCCTGGG
Found at i:1413307 original size:21 final size:21
Alignment explanation
Indices: 1413282--1413336 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1413272 GGAATCGGTA
1413282 CCCCCTTGGGGGGGAATTTGTT
1 CCCCC-TGGGGGGGAATTTGTT
*
1413304 CCCCCTGGGGTGGAATTTGTT
1 CCCCCTGGGGGGGAATTTGTT
1413325 CCCCCTGGGGGG
1 CCCCCTGGGGGG
1413337 AATCTATACC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.07, C:0.27, G:0.38, T:0.27
Consensus pattern (21 bp):
CCCCCTGGGGGGGAATTTGTT
Found at i:1413422 original size:21 final size:20
Alignment explanation
Indices: 1413383--1413420 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1413373 AAAAACCTAC
1413383 GGGGGGAATCTATACCCCTT
1 GGGGGGAATCTATACCCCTT
*
1413403 GGGGGGAATCTGTACCCC
1 GGGGGGAATCTATACCCC
1413421 CTGGACAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCTATACCCCTT
Found at i:1413491 original size:30 final size:30
Alignment explanation
Indices: 1413455--1413514 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1413445 TTTGAAACGG
1413455 TTCGAAATACTTTGTAAAATTGTTTTAAAA
1 TTCGAAATACTTTGTAAAATTGTTTTAAAA
1413485 TTCGAAATACTTTGTAAAATTGTTTTAAAA
1 TTCGAAATACTTTGTAAAATTGTTTTAAAA
1413515 ATAGTTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (30 bp):
TTCGAAATACTTTGTAAAATTGTTTTAAAA
Found at i:1431399 original size:32 final size:32
Alignment explanation
Indices: 1431356--1431434 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 32
1431346 TTAATTCTTA
* *
1431356 ACATATCATATATTATGTCATCACTTTAAATG
1 ACATAACATATATTATATCATCACTTTAAATG
* * * * *
1431388 ATATAATATATATCATATCATTATTTTAAATG
1 ACATAACATATATTATATCATCACTTTAAATG
*
1431420 ACATGACATATATTA
1 ACATAACATATATTA
1431435 AGTAACATAA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (32 bp):
ACATAACATATATTATATCATCACTTTAAATG
Found at i:1435768 original size:27 final size:24
Alignment explanation
Indices: 1435704--1435750 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1435694 ACGACTTTCT
*
1435704 AAATATTTTTTTTTTATTAAAATC
1 AAATATATTTTTTTTATTAAAATC
1435728 AAATATATTTTTTTTATTAAAAT
1 AAATATATTTTTTTTATTAAAAT
1435751 TGTAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATATATTTTTTTTATTAAAATC
Found at i:1435882 original size:22 final size:22
Alignment explanation
Indices: 1435851--1435900 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1435841 AATAAATAAT
* *
1435851 TAAAAATTAT-TTTTTCTATTAG
1 TAAAAATTATATCTTTC-ATTAA
*
1435873 TAAAAGTTATATCTTTCATTAA
1 TAAAAATTATATCTTTCATTAA
1435895 TAAAAA
1 TAAAAA
1435901 ATAAAACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (22 bp):
TAAAAATTATATCTTTCATTAA
Found at i:1437170 original size:17 final size:17
Alignment explanation
Indices: 1437150--1437206 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
1437140 ATAATTATAT
*
1437150 AAAACAAGAAAGTAAAG
1 AAAAAAAGAAAGTAAAG
**
1437167 AAAAAAAGAAA-TATTG
1 AAAAAAAGAAAGTAAAG
1437183 ACAAAAAAGAAAGATAAAG
1 A-AAAAAAGAAAG-TAAAG
1437202 AAAAA
1 AAAAA
1437207 GATAAATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.12
17 20 0.62
18 4 0.12
19 4 0.12
ACGTcount: A:0.74, C:0.04, G:0.14, T:0.09
Consensus pattern (17 bp):
AAAAAAAGAAAGTAAAG
Found at i:1437972 original size:2 final size:2
Alignment explanation
Indices: 1437965--1438015 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1437955 AAAGAATTAC
1437965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1438007 AT AT AT AT A
1 AT AT AT AT A
1438016 ATGATACTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1441129 original size:13 final size:13
Alignment explanation
Indices: 1441111--1441178 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
1441101 TGAGCTTGAA
1441111 TCGAGCTCGAGTC
1 TCGAGCTCGAGTC
* *
1441124 TCGAGCTTGA--A
1 TCGAGCTCGAGTC
1441135 TCGAGCTCGAGTC
1 TCGAGCTCGAGTC
*
1441148 TCGAGCTTC-A--A
1 TCGAGC-TCGAGTC
1441159 TCGAGCTCGAGTC
1 TCGAGCTCGAGTC
1441172 TCGAGCT
1 TCGAGCT
1441179 TCAATCAAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
10 2 0.05
11 16 0.37
13 23 0.53
14 2 0.05
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (13 bp):
TCGAGCTCGAGTC
Found at i:1441131 original size:24 final size:24
Alignment explanation
Indices: 1441094--1441190 Score: 151
Period size: 24 Copynumber: 4.1 Consensus size: 24
1441084 CGAGTTTGAA
* *
1441094 TCGAGT-TTGAGCTTGAATCGAGC
1 TCGAGTCTCGAGCTTCAATCGAGC
*
1441117 TCGAGTCTCGAGCTTGAATCGAGC
1 TCGAGTCTCGAGCTTCAATCGAGC
1441141 TCGAGTCTCGAGCTTCAATCGAGC
1 TCGAGTCTCGAGCTTCAATCGAGC
*
1441165 TCGAGTCTCGAGCTTCAATCAAGC
1 TCGAGTCTCGAGCTTCAATCGAGC
1441189 TC
1 TC
1441191 CAGAATTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
23 6 0.09
24 64 0.91
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.27
Consensus pattern (24 bp):
TCGAGTCTCGAGCTTCAATCGAGC
Found at i:1441145 original size:17 final size:17
Alignment explanation
Indices: 1441060--1441121 Score: 97
Period size: 17 Copynumber: 3.6 Consensus size: 17
1441050 AAATTCGAGT
1441060 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
*
1441077 TCGAGTTCGAGTTTGAA
1 TCGAGTTCGAGCTTGAA
*
1441094 TCGAGTTTGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
*
1441111 TCGAGCTCGAG
1 TCGAGTTCGAG
1441122 TCTCGAGCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.31
Consensus pattern (17 bp):
TCGAGTTCGAGCTTGAA
Found at i:1447741 original size:15 final size:15
Alignment explanation
Indices: 1447721--1447757 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1447711 TGAGACATTG
*
1447721 CCCGCCCCGCTTCCA
1 CCCGCCCCGCATCCA
*
1447736 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCA
1447751 CCCGCCC
1 CCCGCCC
1447758 GCCCAGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.70, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCGCATCCA
Found at i:1452537 original size:31 final size:31
Alignment explanation
Indices: 1452484--1452543 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1452474 TAATAAAGTT
*
1452484 TAATGACTTATGGTATAATTTACCCTTTTCC
1 TAATGACTCATGGTATAATTTACCCTTTTCC
* * * *
1452515 TAATGACTCGTGGTGTAGTTTACTCTTTT
1 TAATGACTCATGGTATAATTTACCCTTTT
1452544 TTTCCTTATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.47
Consensus pattern (31 bp):
TAATGACTCATGGTATAATTTACCCTTTTCC
Found at i:1453484 original size:31 final size:32
Alignment explanation
Indices: 1453447--1453507 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1453437 AGTTTAAATT
* * *
1453447 TTTTAATTTAATTACT-TGACTTTCCAATTAC
1 TTTTAATTCAATCACTCTGACTTTCAAATTAC
1453478 TTTTAATTCAATCACTCTGACTTTCAAATT
1 TTTTAATTCAATCACTCTGACTTTCAAATT
1453508 TTTTTATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.49
Consensus pattern (32 bp):
TTTTAATTCAATCACTCTGACTTTCAAATTAC
Found at i:1453513 original size:31 final size:30
Alignment explanation
Indices: 1453445--1453519 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
1453435 AAAGTTTAAA
* * *
1453445 TTTTTTAATTTAATTACTTGACTTTCCAAT
1 TTTTTTAATTCAATCACTTGACTTTCAAAT
*
1453475 TACTTTTAATTCAATCACTCTGACTTTCAAAT
1 T-TTTTTAATTCAATCACT-TGACTTTCAAAT
*
1453507 TTTTTTATTTCAA
1 TTTTTTAATTCAA
1453520 AATTATAGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 1 0.03
31 24 0.65
32 12 0.32
ACGTcount: A:0.28, C:0.16, G:0.03, T:0.53
Consensus pattern (30 bp):
TTTTTTAATTCAATCACTTGACTTTCAAAT
Found at i:1459616 original size:13 final size:13
Alignment explanation
Indices: 1459598--1459624 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1459588 AAACATAATT
1459598 TTATTTCCATAAA
1 TTATTTCCATAAA
1459611 TTATTTCCATAAA
1 TTATTTCCATAAA
1459624 T
1 T
1459625 AGACCGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATTTCCATAAA
Found at i:1463375 original size:2 final size:2
Alignment explanation
Indices: 1463370--1463401 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1463360 AAAAATTACA
1463370 AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1463402 GTAAGATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Done.