Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold382
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: 2572505
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 8 of 16
Found at i:1176386 original size:289 final size:287
Alignment explanation
Indices: 1175801--1176389 Score: 796
Period size: 289 Copynumber: 2.0 Consensus size: 287
1175791 TCTCCGCAAT
* *
1175801 CGGGGATATTCTC-ACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCA
1 CGGGGATACTC-CAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCA
*
1175865 ACTCCGATTTTATTTCCAAAAAACACCAATTTTTTCATCAGGGATACTCCAACCCTGTTAATCAT
65 ACTCCGATTTTATTTCCAAAAAACACCAATTTTTACATCAGGGATACTCCAACCCTGTTAATCAT
* ** ** **
1175930 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTTGCTTTATTCTTAAAATAT
130 CAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
* * *
1175995 TGATTTCTCATAATCGGGGATACTCCAACCCTGTTATTTCCGAAGGGATACTCTAATCCCGGTTT
195 TGATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGATTT
** *
1176060 CATTTATAAAACATCAATTTCTCTTAAT
260 CATTTATAAAACATCAATTTCTCACAAC
* * *
1176088 CGAGGATACTCCAACTTCGATTTTA-TTTCTAAAACACCCATTTT-TCATAATCGGGGATACTCC
1 CGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACCAATTTTCT-ATAATCGGGGATACTCC
1176151 AACTCCGATTTTATTTCC-AAAAACACCAATTTTTCACAATC-GAGGATACTCCAA-CCTCGTTA
64 AACTCCGATTTTATTTCCAAAAAACACCAATTTTT-AC-ATCAG-GGATACTCCAACCCT-GTTA
*
1176213 TTTCATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCA
125 -ATCATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCA
*
1176278 AAATATTGATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCC
189 AAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCC
* * * * ***
1176343 CGATTT-TTTTTTCTAATCATTGCTTTCTCACAAC
254 CGATTTCATTTAT-AAAACATCAATTTCTCACAAC
1176377 CGGGGATACTCCA
1 CGGGGATACTCCA
1176390 GCCCCGTTAT
Statistics
Matches: 264, Mismatches: 29, Indels: 16
0.85 0.09 0.05
Matches are distributed among these distances:
286 22 0.08
287 72 0.27
288 22 0.08
289 148 0.56
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (287 bp):
CGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAA
CTCCGATTTTATTTCCAAAAAACACCAATTTTTACATCAGGGATACTCCAACCCTGTTAATCATC
AGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATT
GATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGATTTC
ATTTATAAAACATCAATTTCTCACAAC
Found at i:1179138 original size:79 final size:79
Alignment explanation
Indices: 1179033--1179205 Score: 249
Period size: 79 Copynumber: 2.2 Consensus size: 79
1179023 GAGATAATAA
*
1179033 CGGGGTTGGAGTATCCACTCGAAAATAACGGGGTTGGAACATCCCCGA-TCCTGAAAAATCGATG
1 CGGGGTTGGAGTATCCACTCGAAAATAACGGGGTTGGAACATCCCCGACT-ATGAAAAATCGATG
*
1179097 ATTTAGAAATAAAAT
65 ATTTAGAAATAAAAC
* * * ** * *
1179112 CGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGACTATGAAAAATTGATGT
1 CGGGGTTGGAGTATCCACTCGAAAATAACGGGGTTGGAACATCCCCGACTATGAAAAATCGATGA
1179177 TTTAGAAATAAAAC
66 TTTAGAAATAAAAC
1179191 CGGGGTTGGAGTATC
1 CGGGGTTGGAGTATC
1179206 TCCGATTAAG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 82 0.99
80 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCACTCGAAAATAACGGGGTTGGAACATCCCCGACTATGAAAAATCGATGA
TTTAGAAATAAAAC
Found at i:1179219 original size:51 final size:51
Alignment explanation
Indices: 1179140--1179258 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 51
1179130 TCGGAAATAA
* *
1179140 CGGGGTTGGAGTATCCCCGACTATGAAAAATTGATGTTTTAGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGACTAAGAAAAATTGATATTTTAGAAATAAAAC
* * *
1179191 CGGGGTTGGAGTATCTCCGATTAAGAAAAATTGATATTTTAGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGACTAAGAAAAATTGATATTTTAGAAATAAAAC
*
1179242 CGGGGTTGGGGTATCCC
1 CGGGGTTGGAGTATCCC
1179259 TTCGAAAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGACTAAGAAAAATTGATATTTTAGAAATAAAAC
Found at i:1179236 original size:130 final size:127
Alignment explanation
Indices: 1179085--1179329 Score: 357
Period size: 130 Copynumber: 1.9 Consensus size: 127
1179075 CCCCGATCCT
* * *
1179085 GAAAAATCGATGATTTAGAAATAAAATCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGA
1 GAAAAATCGATGATTTAGAAATAAAACCGGGATTGGAGTATCCCCTCGAAAATAACGGGATTGGA
1179150 GTATCCCCGACTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCTCCGATTAA
66 GTATCCCCG---ATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCTCCGATTAA
* * * * *
1179215 GAAAAATTGAT-ATTTTAGAAATAAAGCCGGGGTTGGGGTATCCCTTCGAAAATAACGGGATTGG
1 GAAAAATCGATGA-TTTAGAAATAAAACCGGGATTGGAGTATCCCCTCGAAAATAACGGGATTGG
* *
1179279 AGTATCCCTGATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGT
65 AGTATCCCCGATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGT
1179330 GTTCCCTCGA
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
127 40 0.38
129 1 0.01
130 63 0.61
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (127 bp):
GAAAAATCGATGATTTAGAAATAAAACCGGGATTGGAGTATCCCCTCGAAAATAACGGGATTGGA
GTATCCCCGATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCTCCGATTAA
Found at i:1179325 original size:76 final size:76
Alignment explanation
Indices: 1179191--1179413 Score: 236
Period size: 76 Copynumber: 2.9 Consensus size: 76
1179181 GAAATAAAAC
* * * * **
1179191 CGGGGTTGGAGTATCTCCGATTAAGAAAAATTGATATTTTAGAAATAAAGCCGGGGTTGGGGTAT
1 CGGGATTGGAGTATC-CC-ATGATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGGGTAT
1179256 CCCTTCGAAAATAA
64 CCC-TCGAAAATAA
1179270 CGGGATTGGAGTATCCC-TGATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTGT-T
1 CGGGATTGGAGTATCCCATGATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGG-G-GTAT
1179333 CCCTCGAAAATAA
64 CCCTCGAAAATAA
* * * * * * *
1179346 CGGGGTTGGAGTATCCCAAATTATG-AAAAGTCAGTGTTTTGGAAATAAAATCGGAGTTGGAGTA
1 CGGGATTGGAGTATCCC--ATGATGAAAAATTGA-TGTTTTAGAAATAAAATCGGGGTTGGGGTA
1179410 TCCC
63 TCCC
1179414 CGATTATGGA
Statistics
Matches: 124, Mismatches: 13, Indels: 15
0.82 0.09 0.10
Matches are distributed among these distances:
76 61 0.49
77 7 0.06
78 14 0.11
79 42 0.34
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (76 bp):
CGGGATTGGAGTATCCCATGATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGGGTATCC
CTCGAAAATAA
Found at i:1179373 original size:206 final size:207
Alignment explanation
Indices: 1179033--1179463 Score: 544
Period size: 206 Copynumber: 2.1 Consensus size: 207
1179023 GAGATAATAA
*
1179033 CGGGGTTGGAGTATCCACTCGAAAATAACGGGGTTGGAACATCCCCGATCCTGAAAAATCGATGA
1 CGGGGTTGGAGTATCCACTCGAAAATAACGGGATTGGAACATCCCCGA--CTGAAAAATCGATGA
* **
1179098 TTTAGAAATAAAATCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGACTA
64 TTTAGAAATAAAATCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCAAACTA
* * * * *
1179163 TGAAAAAT-TGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCTCCGATTAAGAAAAATTGATA
129 TGAAAAGTCAG-TGTTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTAAGAAAAATGGATA
1179227 TTTTAGAAATAAAGC
193 TTTTAGAAATAAAGC
* ** * * *
1179242 CGGGGTTGGGGTATCC-CTTCGAAAATAACGGGATTGGAGTATCCCTGA-TGAAAAATTGATGTT
1 CGGGGTTGGAGTATCCAC-TCGAAAATAACGGGATTGGAACATCCCCGACTGAAAAATCGATGAT
* * * *
1179305 TTAGAAATAAAATCGGGGTTGGAGTGTTCCCTCGAAAATAACGGGGTTGGAGTATCCCAAATTAT
65 TTAGAAATAAAATCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCAAACTAT
* * * * * *
1179370 GAAAAGTCAGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATGGAAAATGGGTGTT
130 GAAAAGTCAGTGTTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTAAGAAAAATGGATATT
**
1179435 TTAGAAATAAAAT
195 TTAGAAATAAAGC
* *
1179448 CAGAGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1179464 CCGAGATGAA
Statistics
Matches: 190, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
206 147 0.77
207 1 0.01
208 1 0.01
209 41 0.22
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (207 bp):
CGGGGTTGGAGTATCCACTCGAAAATAACGGGATTGGAACATCCCCGACTGAAAAATCGATGATT
TAGAAATAAAATCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCAAACTATG
AAAAGTCAGTGTTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTAAGAAAAATGGATATTT
TAGAAATAAAGC
Found at i:1179465 original size:51 final size:51
Alignment explanation
Indices: 1179350--1179475 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 51
1179340 AAATAACGGG
** * *
1179350 GTTGGAGTATCCCAAATTATGAAAAGTCAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAGTCAGTGTTTTAGAAATAAAATCAGA
**
1179401 GTTGGAGTATCCCCGATTATGGAAAA-TGGGTGTTTTAGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTAT-GAAAAGTCAGTGTTTTAGAAATAAAATCAGA
*
1179452 GTTGGAGTATCCCCGA-GATGAAAA
1 GTTGGAGTATCCCCGATTATGAAAA
1179476 ATCTAGAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
49 5 0.07
50 2 0.03
51 55 0.82
52 5 0.07
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAGTCAGTGTTTTAGAAATAAAATCAGA
Found at i:1181793 original size:20 final size:19
Alignment explanation
Indices: 1181779--1181834 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1181769 GATACGTTGT
1181779 AAAATGTATCAATACAATG
1 AAAATGTATCAATACAATG
*
1181798 AGCAATGTATCAATACAATG
1 A-AAATGTATCAATACAATG
*
1181818 CAAAATGTATCGATACA
1 -AAAATGTATCAATACA
1181835 TCTGGGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.25
Consensus pattern (19 bp):
AAAATGTATCAATACAATG
Found at i:1181891 original size:13 final size:13
Alignment explanation
Indices: 1181873--1181898 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1181863 ACAAAGATCG
1181873 ATGTATCGATACA
1 ATGTATCGATACA
1181886 ATGTATCGATACA
1 ATGTATCGATACA
1181899 TTAAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1185095 original size:23 final size:21
Alignment explanation
Indices: 1185054--1185101 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
1185044 TTACATATGG
*
1185054 AAATAAAAATAAATATATTTT
1 AAATAAAAATAAATATATTGT
1185075 AAATAAGAAA-AATATAGTATTGT
1 AAATAA-AAATAA-ATA-TATTGT
1185098 AAAT
1 AAAT
1185102 TTTGATAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 8 0.35
22 6 0.26
23 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (21 bp):
AAATAAAAATAAATATATTGT
Found at i:1185267 original size:15 final size:15
Alignment explanation
Indices: 1185247--1185281 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1185237 ACATTAAAAT
1185247 TTATATTTTAATAAA
1 TTATATTTTAATAAA
**
1185262 TTATATTTTTGTAAA
1 TTATATTTTAATAAA
1185277 TTATA
1 TTATA
1185282 CTCCAATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTATATTTTAATAAA
Found at i:1189080 original size:23 final size:23
Alignment explanation
Indices: 1189036--1189081 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1189026 TGAAAATAAA
*
1189036 AATAATTCAAGATAAGATAATTT
1 AATAATTCAAGATAAGACAATTT
* *
1189059 AATACTTCAAGATAAGGCAATTT
1 AATAATTCAAGATAAGACAATTT
1189082 TAAAACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (23 bp):
AATAATTCAAGATAAGACAATTT
Found at i:1190967 original size:2 final size:2
Alignment explanation
Indices: 1190960--1190994 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1190950 AATAGATAGA
1190960 AT AT AT AT 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 AT AT AT AT A
1190995 AAGCACATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1191759 original size:13 final size:13
Alignment explanation
Indices: 1191727--1191760 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1191717 TTACTGTCAG
1191727 TTAATAATCAGAT
1 TTAATAATCAGAT
**
1191740 TCGATAATCAGAT
1 TTAATAATCAGAT
1191753 TTAATAAT
1 TTAATAAT
1191761 TACGTTATTA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (13 bp):
TTAATAATCAGAT
Found at i:1192620 original size:18 final size:18
Alignment explanation
Indices: 1192594--1192631 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1192584 TTATAATAAA
* *
1192594 TTATTTAACTAATTAATT
1 TTATATAACAAATTAATT
1192612 TTATATAACAAATTAATT
1 TTATATAACAAATTAATT
1192630 TT
1 TT
1192632 TTATCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATATAACAAATTAATT
Found at i:1200809 original size:17 final size:17
Alignment explanation
Indices: 1200787--1200819 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1200777 AAGTTCGTGA
1200787 CAGTTCTAGATTTGCAG
1 CAGTTCTAGATTTGCAG
*
1200804 CAGTTCTATATTTGCA
1 CAGTTCTAGATTTGCA
1200820 TGGTAAGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (17 bp):
CAGTTCTAGATTTGCAG
Found at i:1201449 original size:24 final size:24
Alignment explanation
Indices: 1201406--1201451 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1201396 AATAAAAATT
1201406 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
*
1201430 AGCCACCAATTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
1201452 AAATAACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.20
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:1201489 original size:28 final size:28
Alignment explanation
Indices: 1201456--1201538 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
1201446 AAACAAAAAT
*
1201456 AACCACCATATTTGACAAATATAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
1201484 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
*
1201512 AACTACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
1201539 GTGGCATTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.20
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:1203480 original size:21 final size:22
Alignment explanation
Indices: 1203442--1203487 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1203432 ATCTATTGAA
* **
1203442 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1203463 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1203485 ACT
1 ACT
1203488 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1205893 original size:24 final size:24
Alignment explanation
Indices: 1205865--1205910 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1205855 AATAAAAATT
1205865 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
*
1205889 AGCCACCAATTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
1205911 AAATAACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.20
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:1205948 original size:28 final size:28
Alignment explanation
Indices: 1205915--1205997 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
1205905 AAACAAAAAT
*
1205915 AACCACCATATTTGACAAATATAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
1205943 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
*
1205971 AACTACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
1205998 GTGGCATTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.20
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:1206323 original size:40 final size:40
Alignment explanation
Indices: 1206268--1206388 Score: 233
Period size: 40 Copynumber: 3.0 Consensus size: 40
1206258 ATTATGGAGT
1206268 AACTTTTGAATTGTTAAAACAATTGACATCCGAAGCATTC
1 AACTTTTGAATTGTTAAAACAATTGACATCCGAAGCATTC
*
1206308 AACTTTTGAATTGTTAAAACAATTGACATCCGAAGCAGTC
1 AACTTTTGAATTGTTAAAACAATTGACATCCGAAGCATTC
1206348 AACTTTTGAATTGTTAAAACAATTGACATCCGAAGCATTC
1 AACTTTTGAATTGTTAAAACAATTGACATCCGAAGCATTC
1206388 A
1 A
1206389 TTTTATTTCA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (40 bp):
AACTTTTGAATTGTTAAAACAATTGACATCCGAAGCATTC
Found at i:1209305 original size:26 final size:25
Alignment explanation
Indices: 1209248--1209334 Score: 77
Period size: 28 Copynumber: 3.4 Consensus size: 25
1209238 AGTCACCAAT
* * *
1209248 TTTGACAAAC-AACAAGCCACCATT
1 TTTGACAAACAAAAAAACCACCATA
*
1209272 TTTTACAAACAAAAATAACCACCATA
1 TTTGACAAACAAAAA-AACCACCATA
*
1209298 TTTGACAAATACAAAGGAAACCACCATA
1 TTTGAC-AA-ACAAA-AAAACCACCATA
*
1209326 TTTGGCAAA
1 TTTGACAAA
1209335 TACAAAAGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
24 9 0.18
25 3 0.06
26 14 0.27
27 4 0.08
28 20 0.39
29 1 0.02
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.22
Consensus pattern (25 bp):
TTTGACAAACAAAAAAACCACCATA
Found at i:1209311 original size:28 final size:27
Alignment explanation
Indices: 1209264--1209341 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 27
1209254 AAACAACAAG
* *
1209264 CCACCATTTTTTAC-AA-ACAAAAATAA
1 CCACCATATTTGACAAATACAAAAA-AA
*
1209290 CCACCATATTTGACAAATACAAAGGAAA
1 CCACCATATTTGACAAATACAAA-AAAA
*
1209318 CCACCATATTTGGCAAATACAAAA
1 CCACCATATTTGACAAATACAAAA
1209342 GGTGGCATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
26 12 0.27
27 2 0.05
28 29 0.66
29 1 0.02
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.22
Consensus pattern (27 bp):
CCACCATATTTGACAAATACAAAAAAA
Found at i:1211284 original size:21 final size:22
Alignment explanation
Indices: 1211246--1211291 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1211236 ATCTGTTGAA
* **
1211246 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1211267 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1211289 ACT
1 ACT
1211292 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1212859 original size:17 final size:17
Alignment explanation
Indices: 1212837--1212877 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
1212827 TCTATCAAAG
1212837 CTTCCTTGTTTGTCCTT
1 CTTCCTTGTTTGTCCTT
1212854 CTTCCTTGTTTGTCCTT
1 CTTCCTTGTTTGTCCTT
1212871 CTTCCTT
1 CTTCCTT
1212878 AGTTCATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.00, C:0.32, G:0.10, T:0.59
Consensus pattern (17 bp):
CTTCCTTGTTTGTCCTT
Found at i:1213873 original size:24 final size:24
Alignment explanation
Indices: 1213845--1213890 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1213835 AATAAAAATT
1213845 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* *
1213869 AGCCACCATTTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
1213891 AAATAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:1213918 original size:28 final size:28
Alignment explanation
Indices: 1213871--1213948 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
1213861 AAACAACAAG
* *
1213871 CCACCATTTTTTAC-AA-ACAAA-AATAA
1 CCACCATATTTGACAAATACAAAGAA-AA
*
1213897 CCACCATATTTGACAAATACAAAGGAAA
1 CCACCATATTTGACAAATACAAAGAAAA
1213925 CCACCATATTTGACAAATACAAAG
1 CCACCATATTTGACAAATACAAAG
1213949 TGTGGCATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 12 0.26
27 2 0.04
28 31 0.67
29 1 0.02
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.22
Consensus pattern (28 bp):
CCACCATATTTGACAAATACAAAGAAAA
Found at i:1220595 original size:21 final size:21
Alignment explanation
Indices: 1220569--1220612 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1220559 GAAAATGGAT
1220569 TATGTGATTCTTACTTCTATA
1 TATGTGATTCTTACTTCTATA
1220590 TATGTGATTCTTACTTCTATA
1 TATGTGATTCTTACTTCTATA
1220611 TA
1 TA
1220613 GTTGAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (21 bp):
TATGTGATTCTTACTTCTATA
Found at i:1220781 original size:37 final size:38
Alignment explanation
Indices: 1220740--1220828 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 38
1220730 GTTACAATCA
* *
1220740 TGCCATCGGTTAA-AAGAGTGATTTTTGTTTTGACCCG
1 TGCCATCGGTTAAGAAGAGTGATTTTTGTTCTGAACCG
* * * *
1220777 TGCCACCGG-TAAGAATAGTGGTTTTTGTTCTGAACTG
1 TGCCATCGGTTAAGAAGAGTGATTTTTGTTCTGAACCG
*
1220814 TGCCATCGATTAAGA
1 TGCCATCGGTTAAGA
1220829 TTAGTAGTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
36 3 0.07
37 34 0.81
38 5 0.12
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (38 bp):
TGCCATCGGTTAAGAAGAGTGATTTTTGTTCTGAACCG
Found at i:1220893 original size:38 final size:38
Alignment explanation
Indices: 1220786--1220894 Score: 114
Period size: 38 Copynumber: 2.9 Consensus size: 38
1220776 GTGCCACCGG
* * * * *
1220786 TAAGAATAGTGGTTTTTGTTCTGAA-CTGTGCCATCGAT
1 TAAGAATAGTAGTTTTTGTTCT-AACCTATACCACCAAT
* *
1220824 TAAGATTAGTAGTTTTTGTTTCGAACC-ATACCACCAAT
1 TAAGAATAGTAGTTTTTG-TTCTAACCTATACCACCAAT
*
1220862 TGAGAATAGTAGTTTTTGTTCTAACCTATACCA
1 TAAGAATAGTAGTTTTTGTTCTAACCTATACCA
1220895 TAGGGGTTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
37 7 0.12
38 47 0.81
39 4 0.07
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (38 bp):
TAAGAATAGTAGTTTTTGTTCTAACCTATACCACCAAT
Found at i:1226667 original size:16 final size:15
Alignment explanation
Indices: 1226635--1226669 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1226625 AAATATCTTG
*
1226635 TAAAAAAATAAAGAT
1 TAAAAAAATAAAAAT
1226650 TAAAAAAATAAATAAT
1 TAAAAAAATAAA-AAT
1226666 TAAA
1 TAAA
1226670 TTAAACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
TAAAAAAATAAAAAT
Found at i:1227892 original size:184 final size:184
Alignment explanation
Indices: 1227394--1227948 Score: 1013
Period size: 185 Copynumber: 3.0 Consensus size: 184
1227384 CGTGAATTTA
* *
1227394 AAAAATAATCATAAAT-ACTATACTTAAAGTGTTCTATTACAAAATTGACATTTTTTTTGAAATC
1 AAAAATAATCATAAATGA-TATACTTAAAGTGTTCTATTACACAATTTACA-TTTTTTTGAAATC
* *
1227458 TAAATTTCCAAATGCAACCTTAAAAAATTATAATAAATGGACTAAAAATCTAATAGAACAAAACA
64 TAAATTTCCAAATGCAACCTTAAAAAAATATAATAACTGGACTAAAAATCTAATAGAACAAAACA
1227523 AAATAAAGAAAAATAAAAAAAATTATTAGACTAAGTAAATAAGAACCCAATTAGTT
129 AAATAAAGAAAAATAAAAAAAATTATTAGACTAAGTAAATAAGAACCCAATTAGTT
*
1227579 AAAAATAATCATAAATGATATACTTAAAGTGTTCTGTTACACAATTTACATTTTTTTGAAATCTA
1 AAAAATAATCATAAATGATATACTTAAAGTGTTCTATTACACAATTTACATTTTTTTGAAATCTA
1227644 AATTTCCAAATGCAACCTTAAAAAAAATATAATAACTGGACTAAAAATCTAATAGAACAAAACAA
66 AATTTCCAAATGCAACCTT-AAAAAAATATAATAACTGGACTAAAAATCTAATAGAACAAAACAA
1227709 AATAAAGAAAAATAAAAAAAATTATTAGACTAAGTAAATAAGAACCCAATTAGTT
130 AATAAAGAAAAATAAAAAAAATTATTAGACTAAGTAAATAAGAACCCAATTAGTT
1227764 AAAAATAATCATAAATGATATACTTAAAGTGTTCTATTACACAATTTACATTTTTTTGAAATCTA
1 AAAAATAATCATAAATGATATACTTAAAGTGTTCTATTACACAATTTACATTTTTTTGAAATCTA
*
1227829 AATTTCCAAATGCAACCATAAAAAAATATAATAACTGGACTAAAAATCTAATAGAACAAAACAAA
66 AATTTCCAAATGCAACCTTAAAAAAATATAATAACTGGACTAAAAATCTAATAGAACAAAACAAA
*
1227894 ATAAAGAAAAATAAAAAATATTATTAGACTAAGTAAATAAGAACCCAATTAGTT
131 ATAAAGAAAAATAAAAAAAATTATTAGACTAAGTAAATAAGAACCCAATTAGTT
1227948 A
1 A
1227949 CTGGGTTAAG
Statistics
Matches: 360, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
184 134 0.37
185 225 0.62
186 1 0.00
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (184 bp):
AAAAATAATCATAAATGATATACTTAAAGTGTTCTATTACACAATTTACATTTTTTTGAAATCTA
AATTTCCAAATGCAACCTTAAAAAAATATAATAACTGGACTAAAAATCTAATAGAACAAAACAAA
ATAAAGAAAAATAAAAAAAATTATTAGACTAAGTAAATAAGAACCCAATTAGTT
Found at i:1234905 original size:21 final size:20
Alignment explanation
Indices: 1234871--1234911 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1234861 AAAAGTGGTC
1234871 AATTTTTTTCTTTTTCTTTTG
1 AATTTTTTTCTTTTT-TTTTG
1234892 AATTTGTTTT-TTTTTTTTTG
1 AATTT-TTTTCTTTTTTTTTG
1234912 GGAAATCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (20 bp):
AATTTTTTTCTTTTTTTTTG
Found at i:1238676 original size:62 final size:62
Alignment explanation
Indices: 1238605--1238721 Score: 198
Period size: 62 Copynumber: 1.9 Consensus size: 62
1238595 GAAATTTTAT
* *
1238605 AATTGTTTAATTTATTTGAATGGATATTATACTTGGAGACTTTGTTTGTTCTATAATTGTAG
1 AATTGTTTAATTTATTTGAAGGGATAATATACTTGGAGACTTTGTTTGTTCTATAATTGTAG
* *
1238667 AATTGTTTAATTTATTTGAAGGGATAATATATTTGGAGACTTTGTTTGTTTTATA
1 AATTGTTTAATTTATTTGAAGGGATAATATACTTGGAGACTTTGTTTGTTCTATA
1238722 GTATTTCTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.50
Consensus pattern (62 bp):
AATTGTTTAATTTATTTGAAGGGATAATATACTTGGAGACTTTGTTTGTTCTATAATTGTAG
Found at i:1244477 original size:28 final size:28
Alignment explanation
Indices: 1244445--1244528 Score: 159
Period size: 28 Copynumber: 3.0 Consensus size: 28
1244435 GAAGTTGGAT
1244445 AAATTCCATATACTTTTAAATAAACTTA
1 AAATTCCATATACTTTTAAATAAACTTA
1244473 AAATTCCATATACTTTTAAATAAACTTA
1 AAATTCCATATACTTTTAAATAAACTTA
*
1244501 AAATTCCATATACTCTTAAATAAACTTA
1 AAATTCCATATACTTTTAAATAAACTTA
1244529 CACCATGTAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATTCCATATACTTTTAAATAAACTTA
Found at i:1252362 original size:13 final size:13
Alignment explanation
Indices: 1252344--1252369 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1252334 AATGAACATT
1252344 GGATTATCATTTA
1 GGATTATCATTTA
1252357 GGATTATCATTTA
1 GGATTATCATTTA
1252370 TGTACGGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GGATTATCATTTA
Found at i:1253272 original size:2 final size:2
Alignment explanation
Indices: 1253265--1253291 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1253255 AATAGTTAGC
1253265 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 T
1253292 TTACTCAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1254393 original size:20 final size:20
Alignment explanation
Indices: 1254359--1254404 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1254349 AAGAATTGAA
*
1254359 GAGGGATACAAGAGAAGGAT
1 GAGGGATACAAGAGAAGGAG
** *
1254379 GAGGGATACTTGAGATGGAG
1 GAGGGATACAAGAGAAGGAG
1254399 GAGGGA
1 GAGGGA
1254405 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.46, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAAGGAG
Found at i:1258964 original size:20 final size:20
Alignment explanation
Indices: 1258930--1258975 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1258920 AAGAATTGAA
*
1258930 GAGGGATACAAGAGAAGGAT
1 GAGGGATACAAGAGAAGGAG
** *
1258950 GAGGGATACTTGAGATGGAG
1 GAGGGATACAAGAGAAGGAG
1258970 GAGGGA
1 GAGGGA
1258976 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.46, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAAGGAG
Found at i:1262189 original size:183 final size:185
Alignment explanation
Indices: 1261881--1262244 Score: 651
Period size: 183 Copynumber: 2.0 Consensus size: 185
1261871 TTGACATTAG
* * *
1261881 CAAACATAATTAATTTAAGGGAATTTTGTGAAAATTTTTAATTCTAAGTAATTTTATTTTATTCC
1 CAAACATAACTAATTTAAGGGAATTTTGTGAAAATTTTTAATTCCAAATAATTTTATTTTATTCC
*
1261946 TAAACAAAAAGCCTAAAAATAAAAAATTTATCCTAAAATAAGAAAAAAAAGATTGG-AAAAA-AA
66 TAAACAAAAAGACTAAAAATAAAAAATTTATCCTAAAATAAGAAAAAAAAGATTGGAAAAAATAA
*
1262009 ATAAAAATTGATTTTTGACCAAATTAATATTGTTTATCAAATTAATTTGAGGGAT
131 ATAAAAATTGACTTTTGACCAAATTAATATTGTTTATCAAATTAATTTGAGGGAT
*
1262064 CAAACATAACTAATTTAAGGGAATTTTGTGGAAATTTTTAATTCCAAATAATTTTATTTTATTCC
1 CAAACATAACTAATTTAAGGGAATTTTGTGAAAATTTTTAATTCCAAATAATTTTATTTTATTCC
1262129 TAAACAAAAAGACTAAAAATAAAAAATTTATCCTAAAATAAGAAAAAAAAGATTGGAAAAAATAA
66 TAAACAAAAAGACTAAAAATAAAAAATTTATCCTAAAATAAGAAAAAAAAGATTGGAAAAAATAA
*
1262194 ATAAAAATTGACTTTTGACCAAATTAATATTGTTTATTAAATTAATTTGAG
131 ATAAAAATTGACTTTTGACCAAATTAATATTGTTTATCAAATTAATTTGAG
1262245 ATTTCGTCAG
Statistics
Matches: 172, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
183 116 0.67
184 5 0.03
185 51 0.30
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (185 bp):
CAAACATAACTAATTTAAGGGAATTTTGTGAAAATTTTTAATTCCAAATAATTTTATTTTATTCC
TAAACAAAAAGACTAAAAATAAAAAATTTATCCTAAAATAAGAAAAAAAAGATTGGAAAAAATAA
ATAAAAATTGACTTTTGACCAAATTAATATTGTTTATCAAATTAATTTGAGGGAT
Found at i:1264152 original size:23 final size:24
Alignment explanation
Indices: 1264103--1264153 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1264093 AAAAAATATA
1264103 TTTAAAAATACTTCATTCAAAATT
1 TTTAAAAATACTTCATTCAAAATT
* **
1264127 TTTAAATATACTTTTTTC-AAATT
1 TTTAAAAATACTTCATTCAAAATT
1264150 TTTA
1 TTTA
1264154 TCAATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAAAAATACTTCATTCAAAATT
Found at i:1269796 original size:20 final size:20
Alignment explanation
Indices: 1269771--1269895 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
1269761 TTTTAACTAG
1269771 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
1269791 ATGTATCGATACATCTGGGCAAAATGATAGA
1 ATGTATCGATACAT-T--G----A--A-A-A
*
1269822 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
** * * *
1269842 ATGTATCGATATTTTCATAC
1 ATGTATCGATACATTGAAAA
1269862 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
1269882 ATGTATCGATACAT
1 ATGTATCGATACAT
1269896 CTGGGTACTT
Statistics
Matches: 82, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
20 58 0.71
21 1 0.01
22 1 0.01
23 1 0.01
24 1 0.01
27 1 0.01
28 1 0.01
29 1 0.01
30 2 0.02
31 15 0.18
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:1270848 original size:28 final size:28
Alignment explanation
Indices: 1270734--1271250 Score: 412
Period size: 28 Copynumber: 17.5 Consensus size: 28
1270724 CATTAACTTG
* *
1270734 TGTGGGCTTTGAAAAGAGTCACCACCGACT
1 TGTGGGCTTTGAAAAG-GT-GCCACTGACT
* * * * *
1270764 CGTTTGGGCTTTGAAAAAAGTTACCATTGGCT
1 --TGTGGGCTTTG--AAAAGGTGCCACTGACT
* *
1270796 TATGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTG-AAAAGGTGCCACTGACT
1270825 TGTGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
1270853 TGTGGGCTTTGAAAAGAGTTGCCACTGA-T
1 TGTGGGCTTTGAAAAG-G-TGCCACTGACT
*
1270882 TCATGGGCTTTGAAAAGGGTGCCACTGACT
1 T-GTGGGCTTTGAAAA-GGTGCCACTGACT
*
1270912 TGTGGGCTTTG-AAAGAGTGCCATTGACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
1270940 TGTGGGCTTT-AAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
*
1270968 TGTGGACTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* *
1270996 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* **
1271024 TGTGTGAGCTTTGAAATGGGTTGCCACCAACTT
1 TGTG-G-GCTTTGAAA-AGG-TGCCACTGAC-T
* **
1271057 GTGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTGAAA-AGG-TGCCACTGAC-T
* * *
1271089 GTGTGGGATTTGAAATGAGTTGCCACCGACT
1 -TGTGGGCTTTGAAA--AGGTGCCACTGACT
* * *
1271120 TGTATGGGCTTCGAAATGAGTTGCCACCGACTT
1 TG--TGGGCTTTGAAA--AGGTGCCACTGAC-T
* *
1271153 ATGTGGGCTTTGAAATGATGCCACTGACT
1 -TGTGGGCTTTGAAAAGGTGCCACTGACT
*
1271182 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* * * *
1271210 TATGGGCTTTGAAAGGGTACCACTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
1271238 TATGGGCTTTGAA
1 TGTGGGCTTTGAA
1271251 GAGATGAACG
Statistics
Matches: 422, Mismatches: 40, Indels: 50
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.00
28 184 0.44
29 50 0.12
30 56 0.13
31 5 0.01
32 109 0.26
33 5 0.01
34 11 0.03
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:1271218 original size:214 final size:199
Alignment explanation
Indices: 1270794--1271250 Score: 527
Period size: 214 Copynumber: 2.2 Consensus size: 199
1270784 TTACCATTGG
** **
1270794 CTTATGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGG
1 CTTATGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACCAACTTGTGGG
** * * *
1270859 CTTTGAAAAGAGTTGCCACTGATTCATGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGA
65 CTTTGAAAAGAGTTGCCACCAATTCATGGGATTTGAAAAGGGTGCCACCGACTTGTGGGCTTCGA
**
1270924 AAGAGTGCCATTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCC
130 AAGAGTGCCACCGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCC
1270989 ACTGA
195 ACTGA
* * *
1270994 CTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGTGAGCTTTGAAATGGGTTGCCACCAACTTGT
1 CTTATGGGCTTTGAAAGGGTGCCACTGACTTGTG-G-GCTTTGAAA-AGG-TGCCACCAAC-T-T
* * ** * *
1271059 GTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGATTTGAAATGAGTTGCCACCGACTTGTA
60 GTGGGCTTTGAAAAGAGTTGCCACCAA-TT-CATGGGATTTGAAAAG-GGTGCCACCGACTTG--
* * *
1271124 TGGGCTTCGAAATGAGTTGCCACCGACTTATGTGGGCTTTGAAATGATGCCACTGACTTGTGGGC
120 TGGGCTTCGAAA-GAG-TGCCACCGAC-T-TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGAC
*
1271189 TTTGAAAGGGTGCCACTGA
181 TTTGAAAGGATGCCACTGA
* * *
1271208 CTTATGGGCTTTGAAAGGGTACCACTAACTTATGGGCTTTGAA
1 CTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
1271251 GAGATGAACG
Statistics
Matches: 213, Mismatches: 29, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
199 18 0.08
200 13 0.06
201 9 0.04
202 2 0.01
203 8 0.04
204 1 0.00
205 24 0.11
206 2 0.01
207 12 0.06
208 13 0.06
210 11 0.05
211 3 0.01
212 16 0.08
213 2 0.01
214 79 0.37
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (199 bp):
CTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACCAACTTGTGGGC
TTTGAAAAGAGTTGCCACCAATTCATGGGATTTGAAAAGGGTGCCACCGACTTGTGGGCTTCGAA
AGAGTGCCACCGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCCA
CTGA
Found at i:1272518 original size:18 final size:17
Alignment explanation
Indices: 1272497--1272545 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1272487 TTTTTCTTGG
* *
1272497 TTTTTTTTTTGTTTTCTA
1 TTTTTTTATT-TTTTCCA
1272515 TTTTTTTATTTTTTCCA
1 TTTTTTTATTTTTTCCA
*
1272532 TTTTTTTGTTTTTT
1 TTTTTTTATTTTTT
1272546 TTGGGTGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.06, C:0.06, G:0.04, T:0.84
Consensus pattern (17 bp):
TTTTTTTATTTTTTCCA
Found at i:1278360 original size:36 final size:36
Alignment explanation
Indices: 1278319--1278427 Score: 218
Period size: 36 Copynumber: 3.0 Consensus size: 36
1278309 CTGGGACATA
1278319 GACTGGGGCCACCAAATGGTTTTGGAGCAAGGTTTG
1 GACTGGGGCCACCAAATGGTTTTGGAGCAAGGTTTG
1278355 GACTGGGGCCACCAAATGGTTTTGGAGCAAGGTTTG
1 GACTGGGGCCACCAAATGGTTTTGGAGCAAGGTTTG
1278391 GACTGGGGCCACCAAATGGTTTTGGAGCAAGGTTTG
1 GACTGGGGCCACCAAATGGTTTTGGAGCAAGGTTTG
1278427 G
1 G
1278428 TAAAGCTCTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 73 1.00
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.25
Consensus pattern (36 bp):
GACTGGGGCCACCAAATGGTTTTGGAGCAAGGTTTG
Found at i:1286278 original size:20 final size:20
Alignment explanation
Indices: 1286253--1286377 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1286243 TTTTAATTAG
1286253 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
1286273 ATGTATCGATACATCTAGGTAAAAAGACAGA
1 ATGTATCGATACAT-T--G-----A-A-A-A
* *
1286304 ATGTATTGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
1286324 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
1286344 ATGTATCGATACATGGAAAA
1 ATGTATCGATACATTGAAAA
*
1286364 ATGAATCGATACAT
1 ATGTATCGATACAT
1286378 CTAGGTACTT
Statistics
Matches: 82, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
20 59 0.72
21 1 0.01
22 1 0.01
23 2 0.02
28 2 0.02
29 1 0.01
30 2 0.02
31 14 0.17
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:1291136 original size:2 final size:2
Alignment explanation
Indices: 1291131--1291165 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1291121 AAAAAAGAGA
1291131 AT AT AT AT 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 AT AT AT AT A
1291166 CATGCAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1291588 original size:13 final size:13
Alignment explanation
Indices: 1291570--1291594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1291560 ATTTTGCTTA
1291570 GTATCGATACATT
1 GTATCGATACATT
1291583 GTATCGATACAT
1 GTATCGATACAT
1291595 AAACTGGCAG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1292702 original size:2 final size:2
Alignment explanation
Indices: 1292695--1292734 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1292685 AGAAAAGTGT
1292695 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
1292735 AAACATTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1293227 original size:16 final size:13
Alignment explanation
Indices: 1293191--1293225 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1293181 TAAAAAAACA
1293191 TCATAATAAAATT
1 TCATAATAAAATT
1293204 TCATAATAAAATT
1 TCATAATAAAATT
*
1293217 TCACAATAA
1 TCATAATAA
1293226 TATCAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (13 bp):
TCATAATAAAATT
Found at i:1293265 original size:40 final size:40
Alignment explanation
Indices: 1293198--1293273 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
1293188 ACATCATAAT
*
1293198 AAAATTTCATAATAAAATTTCACAATAATATCAAATACTAA
1 AAAATTTCATAACAAAATTTCACAATAA-ATCAAATACTAA
* *
1293239 AAAATTTCA-AACAAAATTTTATAATAAATCAAATA
1 AAAATTTCATAACAAAATTTCACAATAAATCAAATA
1293274 AAAGCGGCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 8 0.25
40 15 0.47
41 9 0.28
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (40 bp):
AAAATTTCATAACAAAATTTCACAATAAATCAAATACTAA
Found at i:1293779 original size:20 final size:20
Alignment explanation
Indices: 1293756--1293828 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1293746 ACAATTCAAA
1293756 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1293776 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1293797 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1293817 GTATCGATACAT
1 GTATCGATACAT
1293829 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1293800 original size:21 final size:21
Alignment explanation
Indices: 1293774--1293849 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1293764 ACATGTTGCA
1293774 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1293795 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1293815 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1293836 TTGTATCGATACAT
1 ATGTATCGATACAT
1293850 TTCTTGGTAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1293807 original size:41 final size:41
Alignment explanation
Indices: 1293756--1293849 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1293746 ACAATTCAAA
*
1293756 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
1293797 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1293838 GTATCGATACAT
1 GTATCGATACAT
1293850 TTCTTGGTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1293906 original size:13 final size:13
Alignment explanation
Indices: 1293888--1293913 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1293878 TACAGCAAGT
1293888 ATGTATCGATACA
1 ATGTATCGATACA
1293901 ATGTATCGATACA
1 ATGTATCGATACA
1293914 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1297994 original size:15 final size:15
Alignment explanation
Indices: 1297974--1298005 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1297964 ATAAAAATGT
*
1297974 TCAAAATGAGGAAGC
1 TCAAAATGAAGAAGC
1297989 TCAAAATGAAGAAGC
1 TCAAAATGAAGAAGC
1298004 TC
1 TC
1298006 CAAACGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (15 bp):
TCAAAATGAAGAAGC
Found at i:1300098 original size:20 final size:21
Alignment explanation
Indices: 1300019--1300097 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
1300009 AATGTCCAAA
*
1300019 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
1300039 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
1300064 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
1300084 TTGTATCGATACAT
1 ATGTATCGATACAT
1300098 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:1300102 original size:13 final size:13
Alignment explanation
Indices: 1300084--1300122 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1300074 ACATTTTTCT
1300084 TTGTATCGATACA
1 TTGTATCGATACA
1300097 TTGTATCGATACA
1 TTGTATCGATACA
*
1300110 CTGTATCGATACA
1 TTGTATCGATACA
1300123 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1302592 original size:20 final size:20
Alignment explanation
Indices: 1302569--1302641 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1302559 ACAATTCAAA
1302569 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1302589 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1302610 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1302630 GTATCGATACAT
1 GTATCGATACAT
1302642 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1302613 original size:21 final size:21
Alignment explanation
Indices: 1302587--1302662 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1302577 ACATGTTGCA
1302587 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1302608 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1302628 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1302649 TTGTATCGATACAT
1 ATGTATCGATACAT
1302663 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1302620 original size:41 final size:41
Alignment explanation
Indices: 1302569--1302662 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1302559 ACAATTCAAA
*
1302569 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
1302610 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1302651 GTATCGATACAT
1 GTATCGATACAT
1302663 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1302719 original size:13 final size:13
Alignment explanation
Indices: 1302701--1302726 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1302691 TACAGCAAGT
1302701 ATGTATCGATACA
1 ATGTATCGATACA
1302714 ATGTATCGATACA
1 ATGTATCGATACA
1302727 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1304329 original size:113 final size:113
Alignment explanation
Indices: 1304131--1304358 Score: 375
Period size: 113 Copynumber: 2.0 Consensus size: 113
1304121 AAATACAAGT
* *
1304131 TGTTAATTCAAATAGATGTGACATTAGTGATAAGGTACACTTATGTTTACGAAAGAAAACTAAGG
1 TGTTAATTCAAATAGATATGACATTAGTGATAAGGTACACTTATGTTTACGAAAGAAAACTAAAG
* *
1304196 TCTGAGTTTATGTATGCTCACTCTCAAAGAGAGGCAACCATAGATCTC
66 TCTGAGTCTATGTATGCTCACTCTCAAACAGAGGCAACCATAGATCTC
*
1304244 TGTTAATTCAAATAGATATGACATTAGTGATAAGGTACATTTATGTTTACGAAAGAAAACTAAAG
1 TGTTAATTCAAATAGATATGACATTAGTGATAAGGTACACTTATGTTTACGAAAGAAAACTAAAG
* * **
1304309 TTTGAGTCTGTGTATGCTCACTCTCAAACAGAGGCAGTCATAGATCTC
66 TCTGAGTCTATGTATGCTCACTCTCAAACAGAGGCAACCATAGATCTC
1304357 TG
1 TG
1304359 ACTTAGATAG
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 106 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (113 bp):
TGTTAATTCAAATAGATATGACATTAGTGATAAGGTACACTTATGTTTACGAAAGAAAACTAAAG
TCTGAGTCTATGTATGCTCACTCTCAAACAGAGGCAACCATAGATCTC
Found at i:1305729 original size:20 final size:20
Alignment explanation
Indices: 1305704--1305760 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1305694 AAGAATTGAA
1305704 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
*
1305724 GAGGGATACAAGAGAAGGAT
1 GAGGGATACAAGAGAGGGAT
1305744 GAGGGATACAAGAGAGG
1 GAGGGATACAAGAGAGG
1305761 ATGCTTAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.05, G:0.44, T:0.09
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:1305944 original size:24 final size:27
Alignment explanation
Indices: 1305871--1305941 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
1305861 AAACAAGCCT
* *
1305871 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
1305899 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
1305926 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1305942 AATGGATGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:1310539 original size:24 final size:27
Alignment explanation
Indices: 1310471--1310534 Score: 103
Period size: 27 Copynumber: 2.3 Consensus size: 27
1310461 AGCCTCAATA
1310471 TTTGACAAATACAAAGGA-AACCACCATT
1 TTTGACAAATACAAA--ATAACCACCATT
1310499 TTTGACAAATACAAAATAACCACCATT
1 TTTGACAAATACAAAATAACCACCATT
1310526 TTTGACAAA
1 TTTGACAAA
1310535 CAAATGGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.54
28 15 0.43
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (27 bp):
TTTGACAAATACAAAATAACCACCATT
Found at i:1311239 original size:14 final size:14
Alignment explanation
Indices: 1311213--1311242 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1311203 GGCATTAATG
1311213 TAATTTAATTTTTT
1 TAATTTAATTTTTT
1311227 TAATTATAATTTTTT
1 TAATT-TAATTTTTT
1311242 T
1 T
1311243 GAAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TAATTTAATTTTTT
Found at i:1315341 original size:81 final size:75
Alignment explanation
Indices: 1315090--1315369 Score: 240
Period size: 81 Copynumber: 3.5 Consensus size: 75
1315080 TGGAGTATCC
* * * *
1315090 CCTC-AAAGATGGTGTGGTTGGAGTATCCCTAGAGATAAAAAAATTCAATGTTTTAGAAAATAAA
1 CCTCGAAA-ATGGTGGGGTTAGAGTATCCCTA-AGAT-GAAAAATTCAATGTTTT-GAAAGTAAA
*
1315154 AAC-GTTGGAGTAT
62 AACAGTTGAAGTAT
* * * * * * *
1315167 CCTTCGAAAACGATGGGGTTAGAGTATCTCCTAAGATGAAAATTTTAGTGTTTTAAAAGTAAAGA
1 CC-TCGAAAATGGTGGGGTTAGAGTATC-CCTAAGATGAAAAATTCAATGTTTTGAAAGTAAAAA
1315232 CAAGGTTGAAGTATT
64 C-A-GTTGAAGTA-T
* * *
1315247 CCCTTGAAAATGGTGGGGTTAGAGTATCCCTAGAGATGAAGAAATTCAATGATTTGGAAGTAAAA
1 -CCTCGAAAATGGTGGGGTTAGAGTATCCCTA-AGATGAA-AAATTCAATGTTTTGAAAGTAAAA
*
1315312 ACGGAGTTGAAATACCT
63 AC--AGTTGAAGTA--T
*
1315329 CCTCGAAAATGGTAGGGTTAGAGTATTCCCTAAGATGAAAA
1 CCTCGAAAATGGTGGGGTTAGAGTA-TCCCTAAGATGAAAA
1315370 TTTTGGTGTT
Statistics
Matches: 163, Mismatches: 27, Indels: 23
0.77 0.13 0.11
Matches are distributed among these distances:
76 9 0.06
77 15 0.09
78 21 0.13
79 19 0.12
80 32 0.20
81 59 0.36
82 8 0.05
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (75 bp):
CCTCGAAAATGGTGGGGTTAGAGTATCCCTAAGATGAAAAATTCAATGTTTTGAAAGTAAAAACA
GTTGAAGTAT
Found at i:1315419 original size:161 final size:155
Alignment explanation
Indices: 1315098--1315471 Score: 384
Period size: 161 Copynumber: 2.4 Consensus size: 155
1315088 CCCCTCAAAG
* * * *
1315098 ATGGTGTGGTTGGAGTATCCCTAGAGATAAAAAAATTCAATGTTTTAGAAAATAAAAACGTTGGA
1 ATGGTGGGGTTGGAGTATCCCTAGAGAT-GAAAAATTCAATG-TTT-GGAAATAAAAACGTTGAA
* *
1315163 GTATCCTTCGAAAACGATGGGGTTAGAGTATCTCCTAAGATGAAAATTTTAGTGTTTTAAAAGTA
63 ATATCCTTCGAAAACGATAGGGTTAGAGTATCTCCTAAGATGAAAATTTTAGTGTTTTAAAAGTA
1315228 AAGACAAGGTTGAAGTATTCCCTTGAAA
128 AAGACAAGGTTGAAGTATTCCCTTGAAA
* *
1315256 ATGGTGGGGTTAGAGTATCCCTAGAGATGAAGAAATTCAATGATTTGGAAGTAAAAACGGAGTTG
1 ATGGTGGGGTTGGAGTATCCCTAGAGATGAA-AAATTCAATG-TTTGGAAATAAAAAC---GTTG
* * *
1315321 AAATA-CCTCCTCGAAAATGGTAGGGTTAGAGTAT-TCCCTAAGATGAAAATTTTGGTG-TTTAG
61 AAATATCCT--TCGAAAACGATAGGGTTAGAGTATCT-CCTAAGATGAAAATTTTAGTGTTTTA-
* **
1315383 GAAAG-AAA-ACAAGGATTGGAGTA-TCTTTTCGAAA
122 -AAAGTAAAGACAAGG-TTGAAGTATTCCCTT-GAAA
** * * *
1315417 ATGACGGGGTTGGAGTAT-CTTTGAGATGAAAAATTCAGTGTTTGGAAAATAAAAA
1 ATGGTGGGGTTGGAGTATCCCTAGAGATGAAAAATTCAATGTTTGG-AAATAAAAA
1315472 TAGGGTTGGA
Statistics
Matches: 182, Mismatches: 22, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
157 12 0.07
158 44 0.24
159 20 0.11
160 32 0.18
161 70 0.38
162 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (155 bp):
ATGGTGGGGTTGGAGTATCCCTAGAGATGAAAAATTCAATGTTTGGAAATAAAAACGTTGAAATA
TCCTTCGAAAACGATAGGGTTAGAGTATCTCCTAAGATGAAAATTTTAGTGTTTTAAAAGTAAAG
ACAAGGTTGAAGTATTCCCTTGAAA
Found at i:1315497 original size:79 final size:78
Alignment explanation
Indices: 1315076--1315527 Score: 287
Period size: 79 Copynumber: 5.7 Consensus size: 78
1315066 GTGAAAATCG
* * * * * * *
1315076 GGGTTGGAGTATCCCCTC-AAAGATGGTGTGGTTGGAGTATCCCTAGAGATAAAAAAATTCAATG
1 GGGTTGGAGTATCCCTTCGAAA-ATGATGGGGTTAGAGTAT-CCTTGAGAT-GAAAAATTCAGTG
*
1315140 TTTTAGAAAAT-AAAAA
63 -TTTGGAAAATAAAAAA
* * * * * *
1315156 -CGTTGGAGTAT-CCTTCGAAAACGATGGGGTTAGAGTATCTCCTAAGATGAAAATTTTAGTGTT
1 GGGTTGGAGTATCCCTTCGAAAATGATGGGGTTAGAGTATC-CTTGAGATGAAAAATTCAGTGTT
*
1315219 T-TAAAAGTAAAGACAA
65 TGGAAAA-TAAA-A-AA
* * * *
1315235 -GGTTGAAGTATTCCCTT-GAAAATGGTGGGGTTAGAGTATCCCTAGAGATGAAGAAATTCAATG
1 GGGTTGGAGTA-TCCCTTCGAAAATGATGGGGTTAGAGTAT-CCTTGAGATGAA-AAATTCAGTG
* *
1315298 ATTTGG-AAGTAAAAAC
63 -TTTGGAAAATAAAAAA
* * * * * * * * **
1315314 GGAGTTGAAATA-CCTCCTCGAAAATGGTAGGGTTAGAGTATTCCCTAAGATGAAAATTTTGGTG
1 GG-GTTGGAGTATCC-CTTCGAAAATGATGGGGTTAGAGTA-TCCTTGAGATGAAAAATTCAGTG
*
1315378 TTTAGGAAAGA-AAACAA
63 TTT-GGAAA-ATAAAAAA
* ** * * *
1315395 GGATTGGAGTATCTTTTCGAAAATGACGGGGTTGGAGTATCTTTGAGATGAAAAATTCAGTGTTT
1 GGGTTGGAGTATCCCTTCGAAAATGATGGGGTTAGAGTATCCTTGAGATGAAAAATTCAGTGTTT
1315460 GGAAAATAAAAATA
66 GGAAAATAAAAA-A
* * *
1315474 GGGTTGGAGTATCCCTTCAAAAATAATGGGGTT-GAAGTATCCTCGAGATGAAAA
1 GGGTTGGAGTATCCCTTCGAAAATGATGGGGTTAG-AGTATCCTTGAGATGAAAA
1315528 TTTTGATATT
Statistics
Matches: 283, Mismatches: 65, Indels: 49
0.71 0.16 0.12
Matches are distributed among these distances:
75 4 0.01
76 4 0.01
77 13 0.05
78 34 0.12
79 94 0.33
80 66 0.23
81 62 0.22
82 6 0.02
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (78 bp):
GGGTTGGAGTATCCCTTCGAAAATGATGGGGTTAGAGTATCCTTGAGATGAAAAATTCAGTGTTT
GGAAAATAAAAAA
Found at i:1318042 original size:20 final size:20
Alignment explanation
Indices: 1318009--1318068 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
1317999 TCAAAAATCC
*
1318009 AGAA-TGTATTGATACAATT
1 AGAACTGTATCGATACAATT
1318028 AGAACTGTATCGATAC-ATT
1 AGAACTGTATCGATACAATT
1318047 -GCAAGCATGTATCGATACAATT
1 AG-AA-C-TGTATCGATACAATT
1318069 TCTTTCCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 1 0.03
19 9 0.26
20 11 0.31
21 11 0.31
22 3 0.09
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (20 bp):
AGAACTGTATCGATACAATT
Found at i:1318159 original size:20 final size:21
Alignment explanation
Indices: 1318134--1318175 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1318124 TTTTTGATAC
*
1318134 ATTCACTTA-TGTATCAATAT
1 ATTCACTTATTATATCAATAT
1318154 ATTCACTTATTATATCAATAT
1 ATTCACTTATTATATCAATAT
1318175 A
1 A
1318176 AATTATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTCACTTATTATATCAATAT
Found at i:1320629 original size:2 final size:2
Alignment explanation
Indices: 1320622--1320649 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1320612 GAATTGTTTA
1320622 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
1320650 TAAAAAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1326997 original size:32 final size:33
Alignment explanation
Indices: 1326961--1327044 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 33
1326951 ACTAGTTAAA
1326961 AATAAAATTAATTAGAATTATTAA-TCAATAAG-
1 AATAAAATTAATTAGAATT-TTAATTCAATAAGT
*
1326993 AATAAAATTAATTA-ATATTTTAATTTAATAAGT
1 AATAAAATTAATTAGA-ATTTTAATTCAATAAGT
*
1327026 AAAAAAATTAATTAAGAAT
1 AATAAAATTAATT-AGAAT
1327045 AAAAAGAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
31 5 0.11
32 24 0.53
33 12 0.27
34 3 0.07
35 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (33 bp):
AATAAAATTAATTAGAATTTTAATTCAATAAGT
Found at i:1336908 original size:33 final size:33
Alignment explanation
Indices: 1336871--1336943 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
1336861 ACTCTTAAGT
1336871 TTGATCATAGATATTATACACTTTTAGTTAACC
1 TTGATCATAGATATTATACACTTTTAGTTAACC
* *
1336904 TTGATCATAGATATTATACACTTTTGGTTAACT
1 TTGATCATAGATATTATACACTTTTAGTTAACC
1336937 TTGATCA
1 TTGATCA
1336944 AATTTCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (33 bp):
TTGATCATAGATATTATACACTTTTAGTTAACC
Found at i:1339622 original size:76 final size:78
Alignment explanation
Indices: 1339540--1339692 Score: 186
Period size: 78 Copynumber: 2.0 Consensus size: 78
1339530 TATTGAAATA
* * * ** * *
1339540 AATTTTAGATTTTTTAATAATG-AA-ACATTTATTGCATACAAA-TATGAAAAATTAAAATTTTT
1 AATTTTAAATTATATAATAATGAAATACATTTATCACATAAAAATTAT-AAAAAATAAAATTTTT
1339602 AATATTAATAGACC
65 AATATTAATAGACC
* *
1339616 AATTTTAAATTATATAATAATGAAATACATTTATCATATAAAAATTATAAAAAATAAATTTTTTA
1 AATTTTAAATTATATAATAATGAAATACATTTATCACATAAAAATTATAAAAAATAAAATTTTTA
*
1339681 ATATTTATAGAC
66 ATATTAATAGAC
1339693 TACTTCTATT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
76 19 0.30
77 2 0.03
78 40 0.62
79 3 0.05
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (78 bp):
AATTTTAAATTATATAATAATGAAATACATTTATCACATAAAAATTATAAAAAATAAAATTTTTA
ATATTAATAGACC
Found at i:1341320 original size:2 final size:2
Alignment explanation
Indices: 1341313--1341339 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1341303 GAATATAGAC
1341313 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
1341340 AATAAAGCAC
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:1344446 original size:21 final size:20
Alignment explanation
Indices: 1344417--1344456 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1344407 TGATAATAAT
1344417 AACTATAAATAAATACTAAG
1 AACTATAAATAAATACTAAG
*
1344437 AACTGATAAATATATACTAA
1 AACT-ATAAATAAATACTAA
1344457 TATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (20 bp):
AACTATAAATAAATACTAAG
Found at i:1345046 original size:2 final size:2
Alignment explanation
Indices: 1344992--1345031 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1344982 ACAAGAAGTG
1344992 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
1345032 ATAATTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1345467 original size:20 final size:20
Alignment explanation
Indices: 1345439--1345481 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1345429 TACAAGAGAA
* *
1345439 GGATGCTTGAGAGGGATGAG
1 GGATACTTGAGAGGGAGGAG
1345459 GGATACTTGAGAGGGAGGAG
1 GGATACTTGAGAGGGAGGAG
1345479 GGA
1 GGA
1345482 GCCTCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.51, T:0.16
Consensus pattern (20 bp):
GGATACTTGAGAGGGAGGAG
Found at i:1345631 original size:24 final size:27
Alignment explanation
Indices: 1345558--1345628 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
1345548 AAACAAGCCT
* *
1345558 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
1345586 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
1345613 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1345629 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:1350042 original size:20 final size:20
Alignment explanation
Indices: 1350017--1350062 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1350007 GGATACAAGA
* *
1350017 GAGGGATGCTTGAGAGGGAT
1 GAGGGATACTTGAGAGGGAG
1350037 GAGGGATACTTGAGAGGGAG
1 GAGGGATACTTGAGAGGGAG
1350057 GAGGGA
1 GAGGGA
1350063 GCCTCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.52, T:0.15
Consensus pattern (20 bp):
GAGGGATACTTGAGAGGGAG
Found at i:1350200 original size:27 final size:28
Alignment explanation
Indices: 1350139--1350209 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 28
1350129 AAACAAGCCT
* *
1350139 CCATATTTGACAAATACAAAAGAAACCA
1 CCATTTTTGACAAACACAAAAGAAACCA
*
1350167 CCATTTTTGACAAACACAAAA-TAACCA
1 CCATTTTTGACAAACACAAAAGAAACCA
1350194 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1350210 AATGGGTGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.23
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAAGAAACCA
Found at i:1354725 original size:73 final size:73
Alignment explanation
Indices: 1354630--1354780 Score: 266
Period size: 73 Copynumber: 2.1 Consensus size: 73
1354620 CAAAAATCAC
* *
1354630 TATTCTTATCGATTGCACAGGTTAGACAAAAACCACTATTCTTAATTGGTAGCATGGCAAAAACC
1 TATTCTTATCGATGGCACAGGTTAGACAAAAACCACTATTCTTAATTGGTAGCATAGCAAAAACC
1354695 ACTATTCT
66 ACTATTCT
* *
1354703 TATTCTTATCGATGGCATAGGTTAGACAAAAATCACTATTCTTAATTGGTAGCATAGCAAAAACC
1 TATTCTTATCGATGGCACAGGTTAGACAAAAACCACTATTCTTAATTGGTAGCATAGCAAAAACC
1354768 ACTATTCT
66 ACTATTCT
1354776 TATTC
1 TATTC
1354781 GGTGGCACAG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (73 bp):
TATTCTTATCGATGGCACAGGTTAGACAAAAACCACTATTCTTAATTGGTAGCATAGCAAAAACC
ACTATTCT
Found at i:1354746 original size:36 final size:36
Alignment explanation
Indices: 1354619--1354746 Score: 98
Period size: 36 Copynumber: 3.5 Consensus size: 36
1354609 ACAGTTCAGA
* *
1354619 ACAAAAATCACTATTCTTATCGATTGCACAGGTTAG
1 ACAAAAATCACTATTCTTATCGATAGCATAGGTTAG
* * * ** *
1354655 ACAAAAACCACTATTCTTAATTGGTAGCAT-GGCAAAA
1 ACAAAAATCACTATTCTT-ATCGATAGCATAGG-TTAG
** * * *
1354692 ACCACTATTC-TTATTCTTATCGATGGCATAGGTTAG
1 A-CAAAAATCACTATTCTTATCGATAGCATAGGTTAG
1354728 ACAAAAATCACTATTCTTA
1 ACAAAAATCACTATTCTTA
1354747 ATTGGTAGCA
Statistics
Matches: 64, Mismatches: 23, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
35 5 0.08
36 37 0.58
37 18 0.28
38 4 0.06
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (36 bp):
ACAAAAATCACTATTCTTATCGATAGCATAGGTTAG
Found at i:1354780 original size:37 final size:37
Alignment explanation
Indices: 1354666--1354780 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
1354656 CAAAAACCAC
*
1354666 TATTCTTAATTGGTAGCATGGCAAAAACCACTATTCT
1 TATTCTTAATTGGTAGCATAGCAAAAACCACTATTCT
* * * *** * ** * *
1354703 TATTCTT-ATCGATGGCATAGGTTAGA-CAAAAATCAC
1 TATTCTTAATTGGTAGCATAGCAAAAACCACTATTC-T
1354739 TATTCTTAATTGGTAGCATAGCAAAAACCACTATTCT
1 TATTCTTAATTGGTAGCATAGCAAAAACCACTATTCT
1354776 TATTC
1 TATTC
1354781 GGTGGCACAG
Statistics
Matches: 52, Mismatches: 23, Indels: 6
0.64 0.28 0.07
Matches are distributed among these distances:
35 5 0.10
36 18 0.35
37 24 0.46
38 5 0.10
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (37 bp):
TATTCTTAATTGGTAGCATAGCAAAAACCACTATTCT
Found at i:1354793 original size:31 final size:31
Alignment explanation
Indices: 1354729--1354850 Score: 147
Period size: 31 Copynumber: 3.9 Consensus size: 31
1354719 ATAGGTTAGA
* * *
1354729 CAAAAATCACTATTCTTAATT-GGTAGCATAG
1 CAAAAACCACTATTCTT-ATTCGGTGGCACAG
1354760 CAAAAACCACTATTCTTATTCGGTGGCACAG
1 CAAAAACCACTATTCTTATTCGGTGGCACAG
* **
1354791 CAAAAACGACTATTCTTATTCGGTGGCATGG
1 CAAAAACCACTATTCTTATTCGGTGGCACAG
* **
1354822 CAAAAATCACTATTCTTAACCGGTGGCAC
1 CAAAAACCACTATTCTTATTCGGTGGCAC
1354851 GGTTCGAAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 3 0.04
31 76 0.96
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (31 bp):
CAAAAACCACTATTCTTATTCGGTGGCACAG
Found at i:1354805 original size:62 final size:62
Alignment explanation
Indices: 1354729--1354850 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
1354719 ATAGGTTAGA
**
1354729 CAAAAATCACTATTCTTAATT-GGTAGCATAGCAAAAACCACTATTCTTATTCGGTGGCACAG
1 CAAAAATCACTATTCTT-ATTCGGTAGCATAGCAAAAACCACTATTCTTAACCGGTGGCACAG
* * *
1354791 CAAAAA-CGACTATTCTTATTCGGTGGCATGGCAAAAATCACTATTCTTAACCGGTGGCAC
1 CAAAAATC-ACTATTCTTATTCGGTAGCATAGCAAAAACCACTATTCTTAACCGGTGGCAC
1354851 GGTTCGAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
61 4 0.08
62 49 0.92
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (62 bp):
CAAAAATCACTATTCTTATTCGGTAGCATAGCAAAAACCACTATTCTTAACCGGTGGCACAG
Found at i:1355598 original size:36 final size:36
Alignment explanation
Indices: 1355558--1355631 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1355548 AAACAATTAA
1355558 AATTTAGAAAAATATATGCTAATGCACAAAATCAGT
1 AATTTAGAAAAATATATGCTAATGCACAAAATCAGT
1355594 AATTTAGAAAAATATATGCTAATGCACAAAATCAGT
1 AATTTAGAAAAATATATGCTAATGCACAAAATCAGT
1355630 AA
1 AA
1355632 CGTAATTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (36 bp):
AATTTAGAAAAATATATGCTAATGCACAAAATCAGT
Found at i:1358183 original size:2 final size:2
Alignment explanation
Indices: 1358178--1358205 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1358168 CCAACACAAA
1358178 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
1358206 TTATTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1367256 original size:20 final size:21
Alignment explanation
Indices: 1367218--1367256 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1367208 ATAAATAAAG
*
1367218 AAATATCTCTTCTTGATTTGC
1 AAATATCTCTTCATGATTTGC
1367239 AAATATCTC-TCATGATTT
1 AAATATCTCTTCATGATTT
1367257 CTATAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (21 bp):
AAATATCTCTTCATGATTTGC
Found at i:1374176 original size:51 final size:50
Alignment explanation
Indices: 1374087--1374364 Score: 227
Period size: 51 Copynumber: 5.9 Consensus size: 50
1374077 AAAAGTCACA
****
1374087 TTTTTACCCAGATGTATCGATACATTGAAAAATGTATCGATACATTCTGT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGT
*
1374137 CTTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACA---TG-
1 -TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGT
** * * *
1374184 ----TA-TGA-ATGTATCGATACATTCTTCAATATATCGATACATTCTAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGT
* * *
1374228 CTTTTTGCTCAGATGTATTGATACATTTTTCAATGTATCGATACA---TG-
1 -TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGT
** *
1374275 ----TA-TGA-ATGTATCGATACATTCTTCAATGTATCGATACATTCTGT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGT
* *
1374319 ATTTTTTCCCAAATGTATCGATACATTTTTCAATGTATCGATACAT
1 -TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1374365 CTAGTTAAAA
Statistics
Matches: 182, Mismatches: 23, Indels: 44
0.73 0.09 0.18
Matches are distributed among these distances:
40 63 0.35
41 3 0.02
42 3 0.02
43 3 0.02
48 3 0.02
49 2 0.01
50 3 0.02
51 102 0.56
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (50 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGT
Found at i:1374177 original size:20 final size:20
Alignment explanation
Indices: 1374149--1374364 Score: 135
Period size: 20 Copynumber: 9.7 Consensus size: 20
1374139 TTTTACCCAG
1374149 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1374169 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1374189 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
1374209 ATATATCGATACATTCTATCTTTTTGCTCA
1 ATGTATCGAT--A--C-A---TTTT--TCA
*
1374239 GATGTATTGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
* * *
1374260 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1374280 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1374300 ATGTATCGATACATTCTGTATTTTTTCCCAA
1 ATGTATCGAT--A--C---A-TTTTT--C-A
1374331 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
1374351 ATGTATCGATACAT
1 ATGTATCGATACAT
1374365 CTAGTTAAAA
Statistics
Matches: 152, Mismatches: 22, Indels: 44
0.70 0.10 0.20
Matches are distributed among these distances:
20 97 0.64
21 4 0.03
22 2 0.01
23 9 0.06
24 3 0.02
25 1 0.01
26 1 0.01
27 3 0.02
28 7 0.05
29 2 0.01
30 4 0.03
31 19 0.12
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1374209 original size:40 final size:40
Alignment explanation
Indices: 1374149--1374313 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
1374139 TTTTACCCAG
*
1374149 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACATGTATGA
*
1374189 ATGTATCGATACATTCTTCAATATATCGATACATTCTATCTTTTTGCTCA
1 ATGTATCGATACATTCTTCAATATATCGATACA-TGTA------TG---A
* * *
1374239 GATGTATTGATACATTTTTCAATGTATCGATACATGTATGA
1 -ATGTATCGATACATTCTTCAATATATCGATACATGTATGA
*
1374280 ATGTATCGATACATTCTTCAATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATATATCGATACAT
1374314 TCTGTATTTT
Statistics
Matches: 106, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
40 64 0.60
41 4 0.04
44 2 0.02
47 2 0.02
50 4 0.04
51 30 0.28
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (40 bp):
ATGTATCGATACATTCTTCAATATATCGATACATGTATGA
Found at i:1374253 original size:91 final size:91
Alignment explanation
Indices: 1374098--1374364 Score: 417
Period size: 91 Copynumber: 2.9 Consensus size: 91
1374088 TTTTACCCAG
****
1374098 ATGTATCGATACATTGAAAAATGTATCGATACATTCTGTCTTTTTACCCAGATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAGATGTATCGATACAT
*
1374163 TTTTCAATATATCGATACATGTATGA
66 TTTTCAATGTATCGATACATGTATGA
* * * * *
1374189 ATGTATCGATACATTCTTCAATATATCGATACATTCTATCTTTTTGCTCAGATGTATTGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAGATGTATCGATACAT
1374254 TTTTCAATGTATCGATACATGTATGA
66 TTTTCAATGTATCGATACATGTATGA
* * *
1374280 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTATTTTTTCCCAAATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAGATGTATCGATACAT
1374345 TTTTCAATGTATCGATACAT
66 TTTTCAATGTATCGATACAT
1374365 CTAGTTAAAA
Statistics
Matches: 159, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 159 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (91 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAGATGTATCGATACAT
TTTTCAATGTATCGATACATGTATGA
Found at i:1380069 original size:20 final size:21
Alignment explanation
Indices: 1380044--1380083 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1380034 TCTAAACAGC
1380044 CCATGTT-CATGCATTTTAAG
1 CCATGTTCCATGCATTTTAAG
1380064 CCATGTTCCATGCATTTTAA
1 CCATGTTCCATGCATTTTAA
1380084 CATGTCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (21 bp):
CCATGTTCCATGCATTTTAAG
Found at i:1383832 original size:32 final size:33
Alignment explanation
Indices: 1383790--1383867 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
1383780 TCTAAAGCTA
* *
1383790 TTAACTTTGATTACAGAT-TTATACACTTTTGG
1 TTAACTTTGATCACAGATGTTATACACTTTTAG
* *
1383822 TTAACCTTGATCATAGATGTTATACACTTTTAG
1 TTAACTTTGATCACAGATGTTATACACTTTTAG
1383855 TTAACTTTGATCA
1 TTAACTTTGATCA
1383868 AATTTCTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 15 0.38
33 25 0.62
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (33 bp):
TTAACTTTGATCACAGATGTTATACACTTTTAG
Found at i:1384022 original size:108 final size:108
Alignment explanation
Indices: 1383827--1384049 Score: 281
Period size: 108 Copynumber: 2.1 Consensus size: 108
1383817 TTTGGTTAAC
1383827 CTTGATCATAGATGTTATACACTTTTAGTTAACTTTGATCAAATTTCTTAAAGTTGTTTGACATG
1 CTTGATCATAGATGTTATACACTTTTAGTTAACTTTGATCAAATTTCTTAAAGTTGTTTGACATG
* * ** *
1383892 GTAGTTTGCTTCTTTC-TTAAAAAAGAAAGTTCTTATGTTATAA
66 ATAGTTTGCATCTTTCACAAAAAAAG-AAGTTCTTATGTTACAA
* * * *
1383935 CTTGATCATAGATGTTATATACTTTT-GATTAATTTTGATTAAATTT-TCTAAGGTTGTTTGACA
1 CTTGATCATAGATGTTATACACTTTTAG-TTAACTTTGATCAAATTTCT-TAAAGTTGTTTGACA
* **
1383998 TGATTGTTTGCATCTTTCACAAAAAAATGGGGTTCTTATGTTACAA
64 TGATAGTTTGCATCTTTCACAAAAAAA-GAAGTTCTTATGTTACAA
1384044 CTTGAT
1 CTTGAT
1384050 TTATTTTATT
Statistics
Matches: 99, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
107 2 0.02
108 70 0.71
109 26 0.26
110 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (108 bp):
CTTGATCATAGATGTTATACACTTTTAGTTAACTTTGATCAAATTTCTTAAAGTTGTTTGACATG
ATAGTTTGCATCTTTCACAAAAAAAGAAGTTCTTATGTTACAA
Found at i:1386258 original size:18 final size:17
Alignment explanation
Indices: 1386226--1386262 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1386216 TATATAATGC
*
1386226 GTATTTTTATTGTATTT
1 GTATTTGTATTGTATTT
1386243 GTATTTGTACTTGTATTT
1 GTATTTGTA-TTGTATTT
1386261 GT
1 GT
1386263 GTATTGGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.16, C:0.03, G:0.16, T:0.65
Consensus pattern (17 bp):
GTATTTGTATTGTATTT
Found at i:1386390 original size:59 final size:62
Alignment explanation
Indices: 1386330--1386441 Score: 153
Period size: 59 Copynumber: 1.9 Consensus size: 62
1386320 TATTTAAAAT
*
1386330 ATATTTA-AAT-AAATTTTAGAGTTTTTAATAATGAAA-ACATTTA-AAT-TAAAATTTTTA
1 ATATTTATAATCAAATTTTAAAGTTTTTAATAATGAAATACATTTATAATATAAAATTTTTA
* * *
1386387 ATATTTATAGTCTAATTTTAAATTTTTTAATAATGAAATACATTTATAATATAAA
1 ATATTTATAATCAAATTTTAAAGTTTTTAATAATGAAATACATTTATAATATAAA
1386442 TATATAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 7 0.15
58 2 0.04
59 23 0.50
60 7 0.15
61 3 0.07
62 4 0.09
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (62 bp):
ATATTTATAATCAAATTTTAAAGTTTTTAATAATGAAATACATTTATAATATAAAATTTTTA
Found at i:1389655 original size:44 final size:44
Alignment explanation
Indices: 1389518--1389655 Score: 106
Period size: 44 Copynumber: 3.1 Consensus size: 44
1389508 GAATTGAATC
1389518 TGATTCGATTAAAAATTCAATCTTGACAAAATTCAAACCCGAAA
1 TGATTCGATTAAAAATTCAATCTTGACAAAATTCAAACCCGAAA
* * * * * ** * *
1389562 TGATTAGGCTTAAAAAAGGTCAAAC---CCAGGA-TC-AACCATTGAATC
1 TGATT-CGATT-AAAAA-TTCAATCTTGACAAAATTCAAACC--CGAA-A
1389607 TGATTCGATTAAAAATTCAATCTTGACAAAATTCAAACCCGAAA
1 TGATTCGATTAAAAATTCAATCTTGACAAAATTCAAACCCGAAA
1389651 TGATT
1 TGATT
1389656 AGGCTTAAAA
Statistics
Matches: 65, Mismatches: 18, Indels: 22
0.62 0.17 0.21
Matches are distributed among these distances:
42 9 0.14
43 7 0.11
44 19 0.29
45 14 0.22
46 7 0.11
47 9 0.14
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (44 bp):
TGATTCGATTAAAAATTCAATCTTGACAAAATTCAAACCCGAAA
Found at i:1389661 original size:89 final size:89
Alignment explanation
Indices: 1389510--1389687 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 89
1389500 CTGAATTTGA
1389510 ATTGAATCTGATTCGATTAAAAATTCAATCTTGACAAAATTCAAACCCGAAATGATTAGGCTTAA
1 ATTGAATCTGATTCGATTAAAAATTCAATCTTGACAAAATTCAAACCCGAAATGATTAGGCTTAA
*
1389575 AAAAGGTCAAACCCAGGATCAACC
66 AAAAGGTCAAACCCAAGATCAACC
1389599 ATTGAATCTGATTCGATTAAAAATTCAATCTTGACAAAATTCAAACCCGAAATGATTAGGCTTAA
1 ATTGAATCTGATTCGATTAAAAATTCAATCTTGACAAAATTCAAACCCGAAATGATTAGGCTTAA
1389664 AAAAGGTCAAACCCAAGATCAACC
66 AAAAGGTCAAACCCAAGATCAACC
1389688 TGAACCTGAA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (89 bp):
ATTGAATCTGATTCGATTAAAAATTCAATCTTGACAAAATTCAAACCCGAAATGATTAGGCTTAA
AAAAGGTCAAACCCAAGATCAACC
Found at i:1389827 original size:18 final size:18
Alignment explanation
Indices: 1389806--1389840 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1389796 AAATTATTTT
*
1389806 ACAAATTGATTTTATATA
1 ACAAATTAATTTTATATA
1389824 ACAAATTAATTTTATAT
1 ACAAATTAATTTTATAT
1389841 TATTTAAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (18 bp):
ACAAATTAATTTTATATA
Found at i:1393506 original size:13 final size:14
Alignment explanation
Indices: 1393490--1393518 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1393480 ATAATCTTCC
1393490 TAAAT-AATATTTT
1 TAAATAAATATTTT
1393503 TAAATAAATATTTT
1 TAAATAAATATTTT
1393517 TA
1 TA
1393519 TATATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAATAAATATTTT
Found at i:1394701 original size:32 final size:33
Alignment explanation
Indices: 1394663--1394746 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 33
1394653 CTTAATTAAA
*
1394663 AATAAAATTAATTAGAATTATTAA-TTACTAAG-
1 AATAAAATTAATTAGAATT-TTAATTTAATAAGT
1394695 AATAAAATTAATTA-ATATTTTAATTTAATAAGT
1 AATAAAATTAATTAGA-ATTTTAATTTAATAAGT
*
1394728 AAAAAAATTAATTAAGAAT
1 AATAAAATTAATT-AGAAT
1394747 AAAAATAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
31 5 0.11
32 24 0.53
33 12 0.27
34 3 0.07
35 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (33 bp):
AATAAAATTAATTAGAATTTTAATTTAATAAGT
Found at i:1400642 original size:22 final size:21
Alignment explanation
Indices: 1400617--1400659 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1400607 CAATTTGGGT
*
1400617 TAAATTTGATCTTATTCAATTA
1 TAAACTTGAT-TTATTCAATTA
* *
1400639 TAAACTTGCTTTTTTCAATTA
1 TAAACTTGATTTATTCAATTA
1400660 ATCAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.51
Consensus pattern (21 bp):
TAAACTTGATTTATTCAATTA
Found at i:1402256 original size:91 final size:91
Alignment explanation
Indices: 1402155--1402336 Score: 310
Period size: 91 Copynumber: 2.0 Consensus size: 91
1402145 GAAATATATT
** * *
1402155 TATTGGATAAAAACATTAAAAATAAGTCAAAAAAATGTGTTGAACAGCTCCAAGCTGGAGACCTA
1 TATTGGATAAAAACACGAAAAATAAGTAAAAAAAATGTGTTGAACACCTCCAAGCTGGAGACCTA
1402220 GGATAACGCATCCCTAAGCTGATGAC
66 GGATAACGCATCCCTAAGCTGATGAC
* *
1402246 TATTGGATAAATACACGAAACATAAGTAAAAAAAATGTGTTGAACACCTCCAAGCTGGAGACCTA
1 TATTGGATAAAAACACGAAAAATAAGTAAAAAAAATGTGTTGAACACCTCCAAGCTGGAGACCTA
1402311 GGATAACGCATCCCTAAGCTGATGAC
66 GGATAACGCATCCCTAAGCTGATGAC
1402337 GCCAAATGTT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (91 bp):
TATTGGATAAAAACACGAAAAATAAGTAAAAAAAATGTGTTGAACACCTCCAAGCTGGAGACCTA
GGATAACGCATCCCTAAGCTGATGAC
Found at i:1407272 original size:20 final size:20
Alignment explanation
Indices: 1407249--1407301 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
1407239 TTCTTGTTAT
1407249 TTTTATAAATTTTGTTTTAG
1 TTTTATAAATTTTGTTTTAG
* * *
1407269 TTTTATTTAA-TTCGTTTTTG
1 TTTTA-TAAATTTTGTTTTAG
*
1407289 TTTTTTAAATTTT
1 TTTTATAAATTTT
1407302 ATGTAATGAC
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
19 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.70
Consensus pattern (20 bp):
TTTTATAAATTTTGTTTTAG
Found at i:1407368 original size:36 final size:36
Alignment explanation
Indices: 1407328--1407449 Score: 104
Period size: 39 Copynumber: 3.3 Consensus size: 36
1407318 TACTTTTGCG
1407328 TTGATTTTTTGATACTATTACTTTTGCTTTGATTTT
1 TTGATTTTTTGATACTATTACTTTTGCTTTGATTTT
* * * *
1407364 TTGATTTCTTGTTTAGTTTTA-TAAATTTAG-TTTGATTTT
1 TTGATTTTTTG-ATACTATTACT---TTT-GCTTTGATTTT
* * * *
1407403 TTTAATTTTTGATGCCATTACTTTTGCTTTGTATTTT
1 TTGATTTTTTGATACTATTACTTTTGCTTTG-ATTTT
1407440 TTGATTTTTT
1 TTGATTTTTT
1407450 TTATTTTTAT
Statistics
Matches: 64, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
35 1 0.02
36 18 0.28
37 19 0.30
38 4 0.06
39 21 0.33
40 1 0.02
ACGTcount: A:0.17, C:0.07, G:0.11, T:0.65
Consensus pattern (36 bp):
TTGATTTTTTGATACTATTACTTTTGCTTTGATTTT
Found at i:1407414 original size:75 final size:74
Alignment explanation
Indices: 1407333--1407475 Score: 225
Period size: 75 Copynumber: 1.9 Consensus size: 74
1407323 TTGCGTTGAT
*
1407333 TTTTTGATACTATTACTTTTGCTTTG-ATTTTTTGATTTCTTGTTTAGTTTTATAAATTTAGTTT
1 TTTTTGATACCATTACTTTTGCTTTGTATTTTTTGATTT-TT-TTTAGTTTTATAAATTTAGTTT
1407397 GATTTTTTTAA
64 GATTTTTTTAA
* * *
1407408 TTTTTGATGCCATTACTTTTGCTTTGTATTTTTTGATTTTTTTTATTTTTATAAATTTAGTTTTA
1 TTTTTGATACCATTACTTTTGCTTTGTATTTTTTGATTTTTTTTAGTTTTATAAATTTAGTTTGA
1407473 TTT
66 TTT
1407476 GAATTTTTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
74 25 0.40
75 26 0.41
76 12 0.19
ACGTcount: A:0.19, C:0.06, G:0.10, T:0.66
Consensus pattern (74 bp):
TTTTTGATACCATTACTTTTGCTTTGTATTTTTTGATTTTTTTTAGTTTTATAAATTTAGTTTGA
TTTTTTTAA
Found at i:1413100 original size:32 final size:33
Alignment explanation
Indices: 1413057--1413124 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
1413047 TTCTAAAACT
* *
1413057 GTTAACTTTGATTACAAAT-TTATACACTTTTG
1 GTTAACCTTGATCACAAATATTATACACTTTTG
* * *
1413089 GTTAACCTTGATCATAGATATTATACATTTTTG
1 GTTAACCTTGATCACAAATATTATACACTTTTG
1413122 GTT
1 GTT
1413125 GACTTTAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (33 bp):
GTTAACCTTGATCACAAATATTATACACTTTTG
Found at i:1413290 original size:108 final size:108
Alignment explanation
Indices: 1413095--1413298 Score: 277
Period size: 108 Copynumber: 1.9 Consensus size: 108
1413085 TTTGGTTAAC
* * *
1413095 CTTGATCATAGATATTATACATTTTTGGTTGACTTTAATCAAATTTATTAAAGTTGTATGACATA
1 CTTGATCATAGATATTATACACTTTTGATTAACTTTAATCAAATTTATTAAAGTTGTATGACATA
**
1413160 GTAGTTTGCTTCTTTCTTAAAAAAGAAAGTTTTTGTGTTACAA
66 GTAGTTTGCTTCTTTCCCAAAAAAGAAAGTTTTTGTGTTACAA
* * * * * *
1413203 CTTGATCATAGATATTATATACTTTTGATTAATTTTGATTAAATTT-TTTAAGATTGTTTGACAT
1 CTTGATCATAGATATTATACACTTTTGATTAACTTTAATCAAATTTATTAAAG-TTGTATGACAT
1413267 -GATAGTTTGCTTCTTTCCCAAAAAAGAAAGTT
65 AG-TAGTTTGCTTCTTTCCCAAAAAAGAAAGTT
1413299 CTTATGCTAT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 6 0.07
108 77 0.93
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (108 bp):
CTTGATCATAGATATTATACACTTTTGATTAACTTTAATCAAATTTATTAAAGTTGTATGACATA
GTAGTTTGCTTCTTTCCCAAAAAAGAAAGTTTTTGTGTTACAA
Found at i:1415780 original size:77 final size:77
Alignment explanation
Indices: 1415615--1415851 Score: 333
Period size: 76 Copynumber: 3.1 Consensus size: 77
1415605 TATTGAAATA
* *
1415615 AATTTTAGATTTTTTACTAATG-AA-ACATTGATC-GCAT-AAAAATATGAAAAATTAAAATTTT
1 AATTTTAAATTTTTTAATAATGAAATACATT-ATCAG-ATAAAAAATAT-AAAAATTAAAATTTT
1415676 TAATATTTATATACT
63 TAATATTTATATACT
*
1415691 AATTTTAAATTTTTTAATAATGAAATACACTTATCAGATAAAAAATATAAAAAATAAAATTTTTA
1 AATTTTAAATTTTTTAATAATGAAATACA-TTATCAGATAAAAAATATAAAAATTAAAATTTTTA
1415756 ATA-TTATATACT
65 ATATTTATATACT
*
1415768 AATTTTAAATTTTTT-ATAATGAAATACATTTATTAGATAAAAAATATAAAAATTAAAATTTTTA
1 AATTTTAAATTTTTTAATAATGAAATACA-TTATCAGATAAAAAATATAAAAATTAAAATTTTTA
*
1415832 ATATTTATAGACT
65 ATATTTATATACT
*
1415845 ACTTTTA
1 AATTTTA
1415852 TTGGATAAAA
Statistics
Matches: 147, Mismatches: 8, Indels: 11
0.89 0.05 0.07
Matches are distributed among these distances:
76 69 0.47
77 40 0.27
78 27 0.18
79 11 0.07
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (77 bp):
AATTTTAAATTTTTTAATAATGAAATACATTATCAGATAAAAAATATAAAAATTAAAATTTTTAA
TATTTATATACT
Found at i:1417435 original size:2 final size:2
Alignment explanation
Indices: 1417428--1417454 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1417418 AATAGATAGA
1417428 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
1417455 AAGCATTTTT
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:1419851 original size:23 final size:22
Alignment explanation
Indices: 1419823--1419881 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
1419813 AACTAAAAAT
*
1419823 AAAAATTAAATAAAAATATTTTA
1 AAAAATTAAATAAAAATA-TATA
*
1419846 AAAAATTAAA-AAATATATATA
1 AAAAATTAAATAAAAATATATA
*
1419867 AAAAACTAAAATAAA
1 AAAAA-TTAAATAAA
1419882 CAAAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 8 0.26
22 10 0.32
23 13 0.42
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAATTAAATAAAAATATATA
Found at i:1419863 original size:22 final size:21
Alignment explanation
Indices: 1419823--1419877 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
1419813 AACTAAAAAT
*
1419823 AAAAATTAAATAAAAATATTTTA
1 AAAAATTAAA-AAAAATA-TATA
*
1419846 AAAAATTAAAAAATATATATA
1 AAAAATTAAAAAAAATATATA
*
1419867 AAAAACTAAAA
1 AAAAATTAAAA
1419878 TAAACAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 13 0.45
22 6 0.21
23 10 0.34
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATTAAAAAAAATATATA
Found at i:1420515 original size:20 final size:20
Alignment explanation
Indices: 1420507--1420563 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
1420497 GATATATTTT
1420507 TTAATGTATCGATACATGTA
1 TTAATGTATCGATACATGTA
*
1420527 TTAATGTATCGATACAT-TC
1 TTAATGTATCGATACATGTA
*
1420546 TTCAATATATCGATACAT
1 TT-AATGTATCGATACAT
1420564 TCTATCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (20 bp):
TTAATGTATCGATACATGTA
Found at i:1420604 original size:91 final size:91
Alignment explanation
Indices: 1420442--1420611 Score: 286
Period size: 91 Copynumber: 1.9 Consensus size: 91
1420432 TACTCAGATA
* * * *
1420442 TATCAATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAGATGTATTGATATATTTT
1 TATCAATACATTCTTCAATATATCGATACATTCTATCTTTTTACCCAGATGTATCGATACATTTT
*
1420507 TTAATGTATCGATACATGTATTAATG
66 TCAATGTATCGATACATGTATTAATG
*
1420533 TATCGATACATTCTTCAATATATCGATACATTCTATCTTTTTACCCAGATGTATCGATACATTTT
1 TATCAATACATTCTTCAATATATCGATACATTCTATCTTTTTACCCAGATGTATCGATACATTTT
1420598 TCAATGTATCGATA
66 TCAATGTATCGATA
1420612 TATCTAGTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 73 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (91 bp):
TATCAATACATTCTTCAATATATCGATACATTCTATCTTTTTACCCAGATGTATCGATACATTTT
TCAATGTATCGATACATGTATTAATG
Done.