Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002616.1 Hibiscus syriacus cultivar Beakdansim tig00005294_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: 1287628
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1174292 original size:36 final size:35
Alignment explanation
Indices: 1174150--1174308 Score: 141
Period size: 36 Copynumber: 4.6 Consensus size: 35
1174140 CTTTGAAAAT
*
1174150 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
1 GTTTCCCTTGAAACAAATTTTGTCTCACTTGAGAC
* *
1174185 ATTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATC
1 -GTTTCCCTTGAAACAAATTTTGTCTCACTTGAGA-C
* ** *
1174222 GTTTCTCTTGAAACACAAAATT-T-TGA---GA-AC
1 GTTTCCCTTGAAACA-AATTTTGTCTCACTTGAGAC
*
1174252 GTTTCCCTTGAAACGAATTTTGTCTCACTTGAGAC
1 GTTTCCCTTGAAACAAATTTTGTCTCACTTGAGAC
* * *
1174287 AGTTTCTCATGAAACAAGTTTT
1 -GTTTCCCTTGAAACAAATTTT
1174309 TGAGACAATT
Statistics
Matches: 97, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
29 4 0.04
30 15 0.15
31 3 0.03
32 2 0.02
34 2 0.02
35 3 0.03
36 63 0.65
37 5 0.05
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (35 bp):
GTTTCCCTTGAAACAAATTTTGTCTCACTTGAGAC
Found at i:1174320 original size:28 final size:28
Alignment explanation
Indices: 1174280--1174338 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
1174270 TTTGTCTCAC
* *
1174280 TTGAGACAGTTTCTCATGAAACAAGTTT
1 TTGAGACAATTTCTCATGAAACAAATTT
*
1174308 TTGAGACAATTTCTCTTGAAACAAATTT
1 TTGAGACAATTTCTCATGAAACAAATTT
1174336 TTG
1 TTG
1174339 TCTCCCTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (28 bp):
TTGAGACAATTTCTCATGAAACAAATTT
Found at i:1174386 original size:167 final size:168
Alignment explanation
Indices: 1174087--1174404 Score: 371
Period size: 167 Copynumber: 1.9 Consensus size: 168
1174077 AAATTTTGTC
* *
1174087 TCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGT
1 TCCCTTGAAACAAAATTTTGTCTCACTTGAGACAGTTTCTCATGAAACATAAACTTTGAAAA-GT
* * * * * *
1174152 TTCCCTTGAAACAAATTTTGTCTCTCTTGAGACATTTTCCCTTGAAACAAATTTTGTCTCCCTTG
65 TTCCCTTGAAACAAATTTTGTCTCCCTTGAGAAATTTTCCCTTAAAACAAACTTCGTATCCCTTG
*
1174217 AGATCG-TTTCTCTTGAAACACAAAATTTTGAGAACGTT
130 AGATAGTTTTCTCTTGAAACACAAAATTTTGAGAACGTT
* ***
1174255 TCCCTTGAAAC-GAATTTTGTCTCACTTGAGACAGTTTCTCATGAAACA-AGTTTTTGAGACAA-
1 TCCCTTGAAACAAAATTTTGTCTCACTTGAGACAGTTTCTCATGAAACATAAACTTTGA-A-AAG
* **
1174317 TTTCTCTTGAAACAAATTTTTGTCTCCCTT-A-AAATGGTTTTTCTTAAAATC-AACTTCGTATC
64 TTTCCCTTGAAACAAA-TTTTGTCTCCCTTGAGAAAT--TTTCCCTTAAAA-CAAACTTCGTATC
*
1174379 GCTTGAGATAGTTTTCTCTTGAAACA
125 CCTTGAGATAGTTTTCTCTTGAAACA
1174405 AAGTTTTGTC
Statistics
Matches: 126, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
165 3 0.02
166 22 0.17
167 73 0.58
168 28 0.22
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (168 bp):
TCCCTTGAAACAAAATTTTGTCTCACTTGAGACAGTTTCTCATGAAACATAAACTTTGAAAAGTT
TCCCTTGAAACAAATTTTGTCTCCCTTGAGAAATTTTCCCTTAAAACAAACTTCGTATCCCTTGA
GATAGTTTTCTCTTGAAACACAAAATTTTGAGAACGTT
Found at i:1174423 original size:38 final size:36
Alignment explanation
Indices: 1174321--1174440 Score: 116
Period size: 37 Copynumber: 3.2 Consensus size: 36
1174311 AGACAATTTC
* * *
1174321 TCTTGAAACAAATTTTTGTCTCCCTTAAAATGGTTTT
1 TCTTAAAACAAA-TTTTGTCTCCCTTGAGATGGTTTT
* * * * *
1174358 TCTTAAAATC-AACTTCGTATCGCTTGAGATAGTTTT
1 TCTTAAAA-CAAATTTTGTCTCCCTTGAGATGGTTTT
*
1174394 CTCTTGAAACAAAGTTTTGTCTCCCTTGAGATGGTTTT
1 -TCTTAAAACAAA-TTTTGTCTCCCTTGAGATGGTTTT
1174432 TCTTAAAAC
1 TCTTAAAAC
1174441 CTACTTCTTC
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
36 18 0.28
37 26 0.41
38 20 0.31
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (36 bp):
TCTTAAAACAAATTTTGTCTCCCTTGAGATGGTTTT
Found at i:1174474 original size:15 final size:15
Alignment explanation
Indices: 1174454--1174494 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1174444 CTTCTTCTTG
1174454 CTTGAGACAGTCTCC
1 CTTGAGACAGTCTCC
*
1174469 CTTGAGACAGTCTCG
1 CTTGAGACAGTCTCC
1174484 CTTGAGACAGT
1 CTTGAGACAGT
1174495 TTTCATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (15 bp):
CTTGAGACAGTCTCC
Found at i:1174558 original size:24 final size:25
Alignment explanation
Indices: 1174521--1174567 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1174511 ATTTATCTCA
* * *
1174521 CTTGAGATAGTTTTTCTT-AAAACC
1 CTTGAGACAATTTTCCTTCAAAACC
1174545 CTTGAGACAATTTTCCTTCAAAA
1 CTTGAGACAATTTTCCTTCAAAA
1174568 TAAAATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (25 bp):
CTTGAGACAATTTTCCTTCAAAACC
Found at i:1174559 original size:61 final size:61
Alignment explanation
Indices: 1174484--1174604 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
1174474 GACAGTCTCG
* * * * * *
1174484 CTTGAGACAGTTTTCATTTAAAACAAAATTTATCTCACTTGAGATAGTTTTTCTTAAAACC
1 CTTGAGACAATTTTCATTCAAAACAAAATTTATCTCACTCGAGAGAGCTTCTCTTAAAACC
* *
1174545 CTTGAGACAATTTTCCTTCAAAATAAAATTTATCTCACTCGAGAGAGCTTCTCTTAAAAC
1 CTTGAGACAATTTTCATTCAAAACAAAATTTATCTCACTCGAGAGAGCTTCTCTTAAAAC
1174605 AAGTTTCTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (61 bp):
CTTGAGACAATTTTCATTCAAAACAAAATTTATCTCACTCGAGAGAGCTTCTCTTAAAACC
Found at i:1175496 original size:136 final size:136
Alignment explanation
Indices: 1175091--1175476 Score: 657
Period size: 136 Copynumber: 2.8 Consensus size: 136
1175081 AGGTGGATCA
* *
1175091 ACATTTTCATTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
*
1175156 GAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGCTTGAG
66 GAGAAGATCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGCTTGAG
1175221 GGATTG
131 GGATTG
1175227 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* ** * *
1175292 GAGAAAAGT-TTGTTCGACCTATCACTCGATTCACAACATTTTGAATCAGTGACACCTCGCTTAA
66 GAGAAGA-TCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGCTTGA
1175356 GGGATTG
130 GGGATTG
*
1175363 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGTGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* *
1175428 GAGAAGATCTTGTTCAACCTATCACTCGATTCATGACACTTCGAATCAG
66 GAGAAGATCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAG
1175477 CAACGTATCA
Statistics
Matches: 233, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
135 1 0.00
136 232 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (136 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
GAGAAGATCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGCTTGAG
GGATTG
Found at i:1177438 original size:17 final size:18
Alignment explanation
Indices: 1177411--1177458 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 18
1177401 GCAGACTAAC
*
1177411 TTTTGTCTTAAAAAATGA
1 TTTTTTCTTAAAAAATGA
1177429 -TTTTTCTT--AAAATGA
1 TTTTTTCTTAAAAAATGA
*
1177444 TTTTTTTTTAAAAAA
1 TTTTTTCTTAAAAAA
1177459 AAAGACGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.28
16 7 0.28
17 7 0.28
18 4 0.16
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (18 bp):
TTTTTTCTTAAAAAATGA
Found at i:1183177 original size:20 final size:20
Alignment explanation
Indices: 1183123--1183168 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1183113 ACAAAACATG
*
1183123 GGTGGCCAGCAAATATTAGT
1 GGTGGCCAACAAATATTAGT
1183143 GGTGGCCAACAAATATTAGT
1 GGTGGCCAACAAATATTAGT
1183163 GGTGGC
1 GGTGGC
1183169 AGTATAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.24
Consensus pattern (20 bp):
GGTGGCCAACAAATATTAGT
Found at i:1183854 original size:3 final size:3
Alignment explanation
Indices: 1183848--1183879 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1183838 ACATTATTAT
1183848 TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1183880 GATAGTATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1184206 original size:52 final size:52
Alignment explanation
Indices: 1184137--1184949 Score: 1383
Period size: 52 Copynumber: 15.6 Consensus size: 52
1184127 TCGCTCTCTA
* * * *
1184137 TTTCTTCAGGGAGTAGAACTCGAACGATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
1184189 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* *
1184241 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
** * *
1184293 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACTAGACTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
1184345 TTTCTTCAGGGACTAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* *
1184397 TTTCATCAAGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* *
1184449 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
1184501 TTTCTTCAGGGATTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
1184553 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* *
1184605 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
1184657 TTTCTTCAGGGACTAGAACTCGAACAATATTCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
1184709 TTTCTTCAGGGACTAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
1184761 TTTCTTCAAGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* * **
1184813 TTTCTTCAGGGACTAGAACTTGAACAATAATCTTCCTACGAGAATGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1184865 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1184917 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
1184950 CCAACGATCG
Statistics
Matches: 715, Mismatches: 46, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 715 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (52 bp):
TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
Found at i:1184359 original size:26 final size:26
Alignment explanation
Indices: 1184236--1184361 Score: 71
Period size: 24 Copynumber: 4.8 Consensus size: 26
1184226 ACGGGTCTGT
1184236 CCAATTTTCTTCAGGGACTAGAACTCGA
1 CCAATTTTCTTCAGGGACTAG-ACT-GA
* ** ** * *
1184264 ACAATAATCTTC--CTACGAGACTGC
1 CCAATTTTCTTCAGGGACTAGACTGA
1184288 CCAATTTTCTTCAGGGACTAGAACTCGA
1 CCAATTTTCTTCAGGGACTAG-ACT-GA
* ** ** *
1184316 ACAATAATCTTC--CTACTAGACTGT
1 CCAATTTTCTTCAGGGACTAGACTGA
1184340 CCAATTTTCTTCAGGGACTAGA
1 CCAATTTTCTTCAGGGACTAGA
1184362 ACTCGAAAAA
Statistics
Matches: 67, Mismatches: 25, Indels: 14
0.63 0.24 0.13
Matches are distributed among these distances:
24 20 0.30
25 6 0.09
26 19 0.28
27 3 0.04
28 19 0.28
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (26 bp):
CCAATTTTCTTCAGGGACTAGACTGA
Found at i:1184898 original size:28 final size:27
Alignment explanation
Indices: 1184815--1184899 Score: 68
Period size: 28 Copynumber: 3.2 Consensus size: 27
1184805 TGCCCAATTT
1184815 TCTTCAGGGACTAGAACTTGAACAATAA
1 TCTTCAGGGACTAGAAC-TGAACAATAA
** * ** **
1184843 TCTTC--CTACGAGAA-TGCCCAATTT
1 TCTTCAGGGACTAGAACTGAACAATAA
1184867 TCTTCAGGGACTAGAACTCGAACAATAA
1 TCTTCAGGGACTAGAACT-GAACAATAA
1184895 TCTTC
1 TCTTC
1184900 CTACGGGTCT
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 11 0.28
26 12 0.31
27 1 0.03
28 15 0.38
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (27 bp):
TCTTCAGGGACTAGAACTGAACAATAA
Found at i:1185004 original size:55 final size:55
Alignment explanation
Indices: 1184945--1185224 Score: 474
Period size: 55 Copynumber: 5.1 Consensus size: 55
1184935 CTCGAACAAT
*
1184945 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
1185000 AATCTTCAACAATCGCGTATGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
1185055 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
1185108 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1185163 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1185218 AATCTTC
1 AATCTTC
1185225 TTTTGCTTCA
Statistics
Matches: 208, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
53 48 0.23
54 4 0.02
55 156 0.75
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:1185155 original size:108 final size:110
Alignment explanation
Indices: 1184945--1185224 Score: 492
Period size: 108 Copynumber: 2.6 Consensus size: 110
1184935 CTCGAACAAT
*
1184945 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1185010 AATCGCGTATGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
66 AATCGCGTATGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
* *
1185055 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTCATC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* * *
1185118 AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
66 AATCGCGTATGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1185163 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
1185225 TTTTGCTTCA
Statistics
Matches: 161, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
108 101 0.63
109 4 0.02
110 56 0.35
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (110 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
AATCGCGTATGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
Found at i:1186532 original size:14 final size:13
Alignment explanation
Indices: 1186513--1186547 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
1186503 TTATTTATTT
1186513 TTTTTTTTTCTTC
1 TTTTTTTTTCTTC
1186526 TTCTTTTTTTCTTC
1 TT-TTTTTTTCTTC
1186540 TTTTTTTT
1 TTTTTTTT
1186548 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTCTTC
Found at i:1186537 original size:8 final size:8
Alignment explanation
Indices: 1186510--1186627 Score: 75
Period size: 8 Copynumber: 14.6 Consensus size: 8
1186500 CTTTTATTTA
1186510 TTTTT-TT
1 TTTTTCTT
1186517 TTTTTCTT
1 TTTTTCTT
1186525 CTTCTTT-TT
1 -TT-TTTCTT
*
1186534 TTCTTCTTT
1 TTTTTC-TT
*
1186543 TTTTTATT
1 TTTTTCTT
*
1186551 TTTTTATT
1 TTTTTCTT
*
1186559 TTTTTCTA
1 TTTTTCTT
*
1186567 TTTTTCTA
1 TTTTTCTT
1186575 TTTTTC--
1 TTTTTCTT
* *
1186581 TATTTCAT
1 TTTTTCTT
1186589 TTTTTCATT
1 TTTTTC-TT
1186598 TTTTTCATT
1 TTTTTC-TT
*
1186607 TTTTTC-A
1 TTTTTCTT
1186614 TTTTTCATT
1 TTTTTC-TT
1186623 TTTTT
1 TTTTT
1186628 TATCTTTAAG
Statistics
Matches: 91, Mismatches: 10, Indels: 18
0.76 0.08 0.15
Matches are distributed among these distances:
6 5 0.05
7 13 0.14
8 39 0.43
9 31 0.34
10 3 0.03
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1186543 original size:28 final size:28
Alignment explanation
Indices: 1186511--1186565 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1186501 TTTTATTTAT
* *
1186511 TTTTTTTTTTTCTTCTTCTTTTTTTCTTC
1 TTTTTTTTATT-TTCTTATTTTTTTCTTC
*
1186540 TTTTTTTTATTTTTTTATTTTTTTCT
1 TTTTTTTTATTTTCTTATTTTTTTCT
1186566 ATTTTTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (28 bp):
TTTTTTTTATTTTCTTATTTTTTTCTTC
Found at i:1186544 original size:11 final size:11
Alignment explanation
Indices: 1186510--1186546 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1186500 CTTTTATTTA
1186510 TTTTTT-TT-T
1 TTTTTTCTTCT
*
1186519 TTTCTTCTTCT
1 TTTTTTCTTCT
1186530 TTTTTTCTTCT
1 TTTTTTCTTCT
1186541 TTTTTT
1 TTTTTT
1186547 TATTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 5 0.21
10 2 0.08
11 17 0.71
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTCTTCT
Found at i:1186591 original size:39 final size:38
Alignment explanation
Indices: 1186504--1186628 Score: 118
Period size: 39 Copynumber: 3.3 Consensus size: 38
1186494 ACCCCCCTTT
* *
1186504 TATTTATTTTTTTTTTTTCTTCTTCTTTTTTTCT-TCTTTT-
1 TATTTA-TTTTTTTATTT-TT-TTCTATTTTTCTAT-TTTTC
1186544 T-TTTATTTTTTTATTTTTTTCTATTTTTCTATTTTTC
1 TATTTATTTTTTTATTTTTTTCTATTTTTCTATTTTTC
* *
1186581 TATTTCATTTTTTCATTTTTTTC-ATTTTTTTCATTTTTC
1 TATTT-ATTTTTTTATTTTTTTCTATTTTTCT-ATTTTTC
1186620 -ATTT-TTTTT
1 TATTTATTTTT
1186629 ATCTTTAAGC
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
36 20 0.26
37 4 0.05
38 24 0.32
39 27 0.36
40 1 0.01
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (38 bp):
TATTTATTTTTTTATTTTTTTCTATTTTTCTATTTTTC
Found at i:1194707 original size:20 final size:20
Alignment explanation
Indices: 1194653--1194698 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1194643 ACAAAACATG
1194653 GGTGGCCAGCAAATATTAGT
1 GGTGGCCAGCAAATATTAGT
1194673 GGTGGCCAGCAAATATTAGT
1 GGTGGCCAGCAAATATTAGT
1194693 GGTGGC
1 GGTGGC
1194699 AGTATAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (20 bp):
GGTGGCCAGCAAATATTAGT
Found at i:1195380 original size:3 final size:3
Alignment explanation
Indices: 1195374--1195405 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1195364 ACATTATTAT
1195374 TAA TAA TAA -AA TAA TAA T-A TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1195406 GATAGTATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1195390 original size:11 final size:11
Alignment explanation
Indices: 1195374--1195404 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1195364 ACATTATTAT
1195374 TAATAATAAAA
1 TAATAATAAAA
*
1195385 TAATAATATAA
1 TAATAATAAAA
1195396 TAATAATAA
1 TAATAATAA
1195405 TGATAGTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:1196274 original size:15 final size:15
Alignment explanation
Indices: 1196250--1196280 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1196240 TATTTATGTA
*
1196250 TTTTATCCTAAAATC
1 TTTTACCCTAAAATC
1196265 TTTTACCCTAAAATC
1 TTTTACCCTAAAATC
1196280 T
1 T
1196281 AAATCCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTTACCCTAAAATC
Found at i:1207646 original size:17 final size:17
Alignment explanation
Indices: 1207612--1207655 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1207602 GTCCTTAGGA
*
1207612 AGCTAGTTAGGTCACTT
1 AGCTAGCTAGGTCACTT
1207629 AGCTAGCTAGGT-ATCTT
1 AGCTAGCTAGGTCA-CTT
*
1207646 AGGTAGCTAG
1 AGCTAGCTAG
1207656 CTAGGTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (17 bp):
AGCTAGCTAGGTCACTT
Found at i:1207652 original size:21 final size:21
Alignment explanation
Indices: 1207628--1207683 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1207618 TTAGGTCACT
*
1207628 TAGCTAGCTAGGTA-TCTTAGG
1 TAGCTAGCTAGGTAGT-GTAGG
*
1207649 TAGCTAGCTAGGTAGTGTATG
1 TAGCTAGCTAGGTAGTGTAGG
1207670 TAGCTAGCTAGGTA
1 TAGCTAGCTAGGTA
1207684 CCTAGTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.32
Consensus pattern (21 bp):
TAGCTAGCTAGGTAGTGTAGG
Found at i:1208411 original size:23 final size:23
Alignment explanation
Indices: 1208362--1208413 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1208352 GAAGTGCCAC
* *
1208362 GTAGAATTGTCCTGAAGGATCGA
1 GTAGAATTGTCCCGAAGGATCCA
1208385 GTAGAATTGTCCCGAAGGA-CCA
1 GTAGAATTGTCCCGAAGGATCCA
1208407 TGTAGAA
1 -GTAGAA
1208414 CCCTCGACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (23 bp):
GTAGAATTGTCCCGAAGGATCCA
Found at i:1208946 original size:22 final size:22
Alignment explanation
Indices: 1208921--1208996 Score: 143
Period size: 22 Copynumber: 3.5 Consensus size: 22
1208911 TCTACACCCA
1208921 GTACCGATACTTCCCTTCTATG
1 GTACCGATACTTCCCTTCTATG
*
1208943 GTACCAATACTTCCCTTCTATG
1 GTACCGATACTTCCCTTCTATG
1208965 GTACCGATACTTCCCTTCTATG
1 GTACCGATACTTCCCTTCTATG
1208987 GTACCGATAC
1 GTACCGATAC
1208997 CTACCTCAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (22 bp):
GTACCGATACTTCCCTTCTATG
Found at i:1222813 original size:16 final size:16
Alignment explanation
Indices: 1222792--1222829 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1222782 AATACATGCC
1222792 AACAAAACTTCAAAAT
1 AACAAAACTTCAAAAT
1222808 AACAAAACTTCAAAAT
1 AACAAAACTTCAAAAT
1222824 AACAAA
1 AACAAA
1222830 CCACCTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.66, C:0.18, G:0.00, T:0.16
Consensus pattern (16 bp):
AACAAAACTTCAAAAT
Found at i:1223221 original size:23 final size:23
Alignment explanation
Indices: 1223195--1223247 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1223185 CTAAGTGCCA
* * *
1223195 CGTAGATTTGTCCCGAAGGATCG
1 CGTAGAATTATCCCCAAGGATCG
*
1223218 CGTAGAATTATCCCCAATGATCG
1 CGTAGAATTATCCCCAAGGATCG
1223241 CGTAGAA
1 CGTAGAA
1223248 CCCTCGAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (23 bp):
CGTAGAATTATCCCCAAGGATCG
Found at i:1223414 original size:19 final size:20
Alignment explanation
Indices: 1223387--1223428 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1223377 ATGCTTATGA
* *
1223387 AATACAATTTAA-GTAAAAT
1 AATAAAATTTAACATAAAAT
1223406 AATAAAATTTAACATAAAAT
1 AATAAAATTTAACATAAAAT
1223426 AAT
1 AAT
1223429 TCAAATAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAAAATTTAACATAAAAT
Found at i:1229784 original size:21 final size:21
Alignment explanation
Indices: 1229760--1229801 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1229750 ACTTCAAGTT
1229760 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1229781 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1229802 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1232829 original size:30 final size:28
Alignment explanation
Indices: 1232793--1232856 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 28
1232783 GCTGCTGGAA
1232793 ACCGGTTTAACCGGTTTTCAACCAGTTCTG
1 ACCGGTTTAACCGG-TTTCAACCAGTT-TG
* *
1232823 ACCGGTTTGACCGGTTTCAACCGGTTTG
1 ACCGGTTTAACCGGTTTCAACCAGTTTG
1232851 ACCGGT
1 ACCGGT
1232857 CTGACCCGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 8 0.25
29 11 0.34
30 13 0.41
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (28 bp):
ACCGGTTTAACCGGTTTCAACCAGTTTG
Found at i:1232861 original size:9 final size:9
Alignment explanation
Indices: 1232793--1232862 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
1232783 GCTGCTGGAA
*
1232793 ACCGGTTTA
1 ACCGGTTTG
*
1232802 ACCGGTTTTCA
1 ACCGG-TTT-G
*
1232813 ACCAGTTCTG
1 ACCGGTT-TG
1232823 ACCGGTTTG
1 ACCGGTTTG
*
1232832 ACCGGTTTCA
1 ACCGGTTT-G
1232842 ACCGGTTTG
1 ACCGGTTTG
*
1232851 ACCGGTCTG
1 ACCGGTTTG
1232860 ACC
1 ACC
1232863 CGACCGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
9 26 0.51
10 19 0.37
11 6 0.12
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1232891 original size:22 final size:22
Alignment explanation
Indices: 1232866--1232927 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
1232856 TCTGACCCGA
1232866 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
1232888 CCGACCCGA--C-A--GTTGAC
1 CCGACCCGACCCGACCGTTGAC
*
1232905 CCGACCCGACCGGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
1232927 C
1 C
1232928 GTTGACCGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 15 0.44
19 1 0.03
20 2 0.06
22 16 0.47
ACGTcount: A:0.19, C:0.47, G:0.24, T:0.10
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:1232927 original size:17 final size:17
Alignment explanation
Indices: 1232868--1232916 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
1232858 TGACCCGACC
1232868 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
1232885 GACCCGACCCGACAGTT
1 GACCCGACCCGACCGTT
1232902 GACCCGACCCGACCG
1 GACCCGACCCGACCG
1232917 GACCGTTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.20, C:0.47, G:0.24, T:0.08
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1232948 original size:7 final size:7
Alignment explanation
Indices: 1232917--1232947 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1232907 GACCCGACCG
1232917 GACCGTT
1 GACCGTT
1232924 GACCGTT
1 GACCGTT
1232931 GACCGTT
1 GACCGTT
*
1232938 GACTGTT
1 GACCGTT
1232945 GAC
1 GAC
1232948 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:1240115 original size:9 final size:9
Alignment explanation
Indices: 1240101--1240194 Score: 62
Period size: 10 Copynumber: 9.8 Consensus size: 9
1240091 GGCTGCTGGA
1240101 AACCGGTTT
1 AACCGGTTT
1240110 AACCGGTTTT
1 AACCGG-TTT
**
1240120 CAACCATTTCT
1 -AACCGGTT-T
*
1240131 GACCGGTTT
1 AACCGGTTT
*
1240140 GACCGGTTT
1 AACCGGTTT
*
1240149 CAACCGGTTCG
1 -AACCGGTT-T
1240160 AACCGGTTT
1 AACCGGTTT
* *
1240169 GACCGGTCTG
1 AACCGGT-TT
1240179 AACCGGTTT
1 AACCGGTTT
*
1240188 GACCGGT
1 AACCGGT
1240195 CCGACCTGAC
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
9 29 0.44
10 32 0.48
11 5 0.08
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1240164 original size:29 final size:28
Alignment explanation
Indices: 1240102--1240194 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
1240092 GCTGCTGGAA
* **
1240102 ACCGGTTTAACCGGTTTTCAACCATTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
1240132 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
1240160 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
1240189 ACCGGT
1 ACCGGT
1240195 CCGACCTGAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
28 7 0.12
29 36 0.64
30 13 0.23
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:1240195 original size:19 final size:19
Alignment explanation
Indices: 1240130--1240195 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
1240120 CAACCATTTC
*
1240130 TGACCGGTTTG-ACCGGTT
1 TGACCGGTCTGAACCGGTT
*
1240148 TCAACCGGT-TCGAACCGGTT
1 T-GACCGGTCT-GAACCGGTT
1240168 TGACCGGTCTGAACCGGTT
1 TGACCGGTCTGAACCGGTT
1240187 TGACCGGTC
1 TGACCGGTC
1240196 CGACCTGACC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.05
19 31 0.74
20 9 0.21
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.27
Consensus pattern (19 bp):
TGACCGGTCTGAACCGGTT
Found at i:1243442 original size:28 final size:28
Alignment explanation
Indices: 1243410--1243497 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 28
1243400 ATAAACTATT
1243410 TATAATTAATATTAAAATAATTATATAA
1 TATAATTAATATTAAAATAATTATATAA
* *
1243438 TATAAATAATATTAATATTAACTTATATTAA
1 TATAATTAATATTAA-AATAA-TTATA-TAA
*
1243469 TATAA-T-ATATT-TAATAATT-TATAA
1 TATAATTAATATTAAAATAATTATATAA
1243493 T-TAAT
1 TATAAT
1243498 ATTAATATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
23 3 0.06
24 4 0.08
25 2 0.04
26 2 0.04
27 4 0.08
28 14 0.27
29 9 0.17
30 6 0.12
31 8 0.15
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
TATAATTAATATTAAAATAATTATATAA
Found at i:1243453 original size:6 final size:6
Alignment explanation
Indices: 1243414--1243567 Score: 63
Period size: 6 Copynumber: 25.3 Consensus size: 6
1243404 ACTATTTATA
*
1243414 ATTAAT ATTAA- AATAATT ATATAAT A-TAA- A-TAAT ATTAAT ATTAA-
1 ATTAAT ATTAAT ATTAA-T AT-TAAT ATTAAT ATTAAT ATTAAT ATTAAT
* * *
1243459 CTT-AT ATTAAT ATAATAT ATTTAAT AATTTAT AATTAAT ATTAAT A-TAAT
1 ATTAAT ATTAAT ATTA-AT A-TTAAT -ATTAAT -ATTAAT ATTAAT ATTAAT
* * * * * * *
1243509 ATATAGT CTATAAA ATTAAT ATTAAT A-TAAA ATATAGT CTATAAA ATTAAT
1 AT-TAAT AT-TAAT ATTAAT ATTAAT ATTAAT AT-TAAT AT-TAAT ATTAAT
1243560 ATTAAT AT
1 ATTAAT AT
1243568 AAACTATATG
Statistics
Matches: 112, Mismatches: 22, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
4 5 0.04
5 21 0.19
6 47 0.42
7 33 0.29
8 6 0.05
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (6 bp):
ATTAAT
Found at i:1243467 original size:16 final size:15
Alignment explanation
Indices: 1243412--1243503 Score: 70
Period size: 14 Copynumber: 6.3 Consensus size: 15
1243402 AAACTATTTA
*
1243412 TAATTAATATTAA-AA
1 TAATT-ATATTAATAT
1243427 TAATTATA-TAATAT
1 TAATTATATTAATAT
* *
1243441 AAATAATATTAATAT
1 TAATTATATTAATAT
1243456 TAACTTATATTAATA-
1 TAA-TTATATTAATAT
1243471 TAA-TATATTTAATA-
1 TAATTATA-TTAATAT
*
1243485 -ATTTATAATTAATAT
1 TAATTAT-ATTAATAT
1243500 TAAT
1 TAAT
1243504 ATAATATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
13 8 0.13
14 25 0.40
15 17 0.27
16 12 0.19
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTATATTAATAT
Found at i:1243529 original size:31 final size:30
Alignment explanation
Indices: 1243491--1243640 Score: 153
Period size: 31 Copynumber: 4.7 Consensus size: 30
1243481 AATAATTTAT
1243491 AATTAATATTAATATAATATATAGTCTATAA
1 AATTAATATTAATATAA-ATATAGTCTATAA
1243522 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATAT-AAATATAGTCTATAA
1243553 AATTAATATTAATATAAACTATATGT-TATAA
1 AATTAATATTAATATAAA-TATA-GTCTATAA
* *
1243584 ATGATATTATATTAATATAAATTATAAT-TA-AGA
1 A--AT-TAATATTAATATAAA-TATAGTCTATA-A
*
1243617 TAATTAACATTAATATAAACTATA
1 -AATTAATATTAATATAAA-TATA
1243641 TAGTACATTA
Statistics
Matches: 105, Mismatches: 6, Indels: 16
0.83 0.05 0.13
Matches are distributed among these distances:
30 3 0.03
31 70 0.67
32 7 0.07
33 6 0.06
34 19 0.18
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (30 bp):
AATTAATATTAATATAAATATAGTCTATAA
Found at i:1243553 original size:14 final size:14
Alignment explanation
Indices: 1243503--1243555 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1243493 TTAATATTAA
*
1243503 TATAATATATAGTC
1 TATAAAATATAGTC
* *
1243517 TATAAAATTAATATTAA
1 TATAAAA-T-ATAGT-C
1243534 TATAAAATATAGTC
1 TATAAAATATAGTC
1243548 TATAAAAT
1 TATAAAAT
1243556 TAATATTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
16 5 0.16
17 7 0.23
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (14 bp):
TATAAAATATAGTC
Found at i:1243574 original size:24 final size:25
Alignment explanation
Indices: 1243529--1243575 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1243519 TAAAATTAAT
**
1243529 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
1243554 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
1243576 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:1243601 original size:65 final size:64
Alignment explanation
Indices: 1243489--1243644 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 64
1243479 TTAATAATTT
*
1243489 ATAATTAATATTAATAT-AA-TATATAGTCTATAAAATTAATATTAATATAAAATATAGTCTATA
1 ATAATTAATATTAATATAAACTATATAGTCTATAAAATTAATATTAATATAAAATATAAT-TA-A
1243552 -
64 G
* *
1243552 A-AATTAATATTAATATAAACTATAT-GT-TATAAATGATATTATATTAATATAAATTATAATTA
1 ATAATTAATATTAATATAAACTATATAGTCTATAAA--AT-TAATATTAATATAAAATATAATTA
1243614 AG
63 AG
*
1243616 ATAATTAACATTAATATAAACTATATAGT
1 ATAATTAATATTAATATAAACTATATAGT
1243645 ACATTAATAT
Statistics
Matches: 81, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
62 21 0.26
63 6 0.07
64 10 0.12
65 42 0.52
66 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (64 bp):
ATAATTAATATTAATATAAACTATATAGTCTATAAAATTAATATTAATATAAAATATAATTAAG
Found at i:1243664 original size:20 final size:21
Alignment explanation
Indices: 1243623--1243664 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1243613 AAGATAATTA
1243623 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
1243645 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
1243665 TCATATAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:1243702 original size:22 final size:22
Alignment explanation
Indices: 1243659--1243702 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1243649 TAATATAAAC
**
1243659 TATAGTTCATATAGTTTATATA
1 TATAGTTCATATAGTAAATATA
1243681 TATAGTTCATAT-GTAAACTATA
1 TATAGTTCATATAGTAAA-TATA
1243703 GTTCATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (22 bp):
TATAGTTCATATAGTAAATATA
Found at i:1243720 original size:18 final size:17
Alignment explanation
Indices: 1243675--1243720 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1243665 TCATATAGTT
1243675 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
1243692 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
1243710 TATATAGTATA
1 TATATA-TATA
1243721 TAAATATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:1243731 original size:33 final size:33
Alignment explanation
Indices: 1243668--1243816 Score: 153
Period size: 33 Copynumber: 4.5 Consensus size: 33
1243658 CTATAGTTCA
*
1243668 TATAGTTTATATATATAGT-TCAT--ATGTAAAC
1 TATAGTTTATATATATAGTAT-ATAAATATAAAC
*
1243699 TATAGTTCATATATATAGTATATAAATATAAAC
1 TATAGTTTATATATATAGTATATAAATATAAAC
* *
1243732 TATAGTTTATATAAATAGTATATAAATATAAAT
1 TATAGTTTATATATATAGTATATAAATATAAAC
* * *
1243765 TATAGTATGTAGATTATATA-AATATAAATATAAATTG
1 TATAGT-T-TATA-TATATAGTATATAAATATAAA--C
1243802 TATAGTTTATATATA
1 TATAGTTTATATATA
1243817 ACTCATATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
31 20 0.20
32 1 0.01
33 43 0.43
34 5 0.05
35 19 0.19
36 6 0.06
37 6 0.06
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (33 bp):
TATAGTTTATATATATAGTATATAAATATAAAC
Found at i:1243735 original size:20 final size:19
Alignment explanation
Indices: 1243711--1243799 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 19
1243701 TAGTTCATAT
1243711 ATATAGTATATAAATATAA
1 ATATAGTATATAAATATAA
1243730 ACTATAGT-T-T--ATAT-A
1 A-TATAGTATATAAATATAA
1243745 A-ATAGTATATAAATATAA
1 ATATAGTATATAAATATAA
*
1243763 ATTATAGTATGTAGATTATATAA
1 A-TATAGTATATA-A--ATATAA
*
1243786 ATATA-AATATAAAT
1 ATATAGTATATAAAT
1243800 TGTATAGTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 23
0.68 0.04 0.28
Matches are distributed among these distances:
13 5 0.09
14 1 0.02
15 3 0.05
16 4 0.07
17 4 0.07
18 5 0.09
19 2 0.04
20 16 0.29
21 5 0.09
22 4 0.07
23 7 0.12
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (19 bp):
ATATAGTATATAAATATAA
Found at i:1243817 original size:20 final size:20
Alignment explanation
Indices: 1243792--1243894 Score: 75
Period size: 20 Copynumber: 5.0 Consensus size: 20
1243782 ATAAATATAA
*
1243792 ATATAAATTGTATAGTTTAT
1 ATATAAATTATATAGTTTAT
* *
1243812 ATATAACTCATATATAATTTAT
1 ATATAAAT--TATATAGTTTAT
* * *
1243834 ATATAAACTATGTAGTTTCT
1 ATATAAATTATATAGTTTAT
* *
1243854 ATAT-AGTTCA-ATAGTTCAT
1 ATATAAATT-ATATAGTTTAT
*
1243873 ATATAAACTATATAGTATTAT
1 ATATAAATTATATAGT-TTAT
1243894 A
1 A
1243895 GTTTATTCAT
Statistics
Matches: 61, Mismatches: 16, Indels: 11
0.69 0.18 0.12
Matches are distributed among these distances:
19 13 0.21
20 28 0.46
21 4 0.07
22 16 0.26
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (20 bp):
ATATAAATTATATAGTTTAT
Found at i:1243972 original size:7 final size:7
Alignment explanation
Indices: 1243957--1244082 Score: 55
Period size: 7 Copynumber: 17.6 Consensus size: 7
1243947 ATATGTAAAT
*
1243957 TATACTA
1 TATAGTA
1243964 TATAGTATA
1 TATAG--TA
1243973 TATAGTTTA
1 TATAG--TA
*
1243982 TATAATA
1 TATAGTA
1243989 TATAGTA
1 TATAGTA
*
1243996 TATAATA
1 TATAGTA
* *
1244003 TAAACTA
1 TATAGTA
1244010 TAGTA-TA
1 TA-TAGTA
1244017 TATAGGTCA
1 TATA-GT-A
1244026 TAT-GTA
1 TATAGTA
*
1244032 -A-ATTA
1 TATAGTA
1244037 TATAGTA
1 TATAGTA
*
1244044 TATA-AA
1 TATAGTA
**
1244050 TATAAAA
1 TATAGTA
1244057 TATAGTA
1 TATAGTA
*
1244064 TATATATA
1 TATA-GTA
1244072 TATAGTA
1 TATAGTA
1244079 TATA
1 TATA
1244083 AATATAAACT
Statistics
Matches: 93, Mismatches: 15, Indels: 22
0.72 0.12 0.17
Matches are distributed among these distances:
5 3 0.03
6 9 0.10
7 55 0.59
8 8 0.09
9 18 0.19
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (7 bp):
TATAGTA
Found at i:1243974 original size:2 final size:2
Alignment explanation
Indices: 1243957--1244121 Score: 68
Period size: 2 Copynumber: 78.0 Consensus size: 2
1243947 ATATGTAAAT
*
1243957 TA TA CTA TA TA GTA TA TA TA GTT TA TA TA -A TA TA TA GTA TA TA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA
* ** * *
1244000 -A TA TA AA CTA TA GTA TA TA TA GG TCA TA TG TA AA T- TA TA TA
1 TA TA TA TA -TA TA -TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
* *
1244041 GTA TA TA AA TA TA -A AA TA TA GTA TA TA TA TA TA TA GTA TA TA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* * * * *
1244083 AA TA TA AA CTA TA GTT TA TA TA AA TA GTA TA TA TT TA TA
1 TA TA TA TA -TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA
1244122 AATTATAGTA
Statistics
Matches: 121, Mismatches: 25, Indels: 34
0.67 0.14 0.19
Matches are distributed among these distances:
1 4 0.03
2 96 0.79
3 21 0.17
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.42
Consensus pattern (2 bp):
TA
Found at i:1243989 original size:14 final size:14
Alignment explanation
Indices: 1243970--1244088 Score: 79
Period size: 14 Copynumber: 8.5 Consensus size: 14
1243960 ACTATATAGT
1243970 ATATATAGTTTATATA
1 ATATATAG--TATATA
1243986 ATATATAGTATATA
1 ATATATAGTATATA
* *
1244000 ATATAAACTATAGT-
1 ATATATAGTATA-TA
1244014 ATATATAGGTCATAT-
1 ATATATA-GT-ATATA
* *
1244029 GTA-A-ATTATATA
1 ATATATAGTATATA
* *
1244041 GTATATA-AATATA
1 ATATATAGTATATA
*
1244054 AAATATAGTATATA
1 ATATATAGTATATA
1244068 TATATATAGTATATA
1 -ATATATAGTATATA
1244083 A-ATATA
1 ATATATA
1244089 AACTATAGTT
Statistics
Matches: 84, Mismatches: 11, Indels: 19
0.74 0.10 0.17
Matches are distributed among these distances:
11 4 0.05
12 4 0.05
13 17 0.20
14 30 0.36
15 18 0.21
16 11 0.13
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.41
Consensus pattern (14 bp):
ATATATAGTATATA
Found at i:1244053 original size:35 final size:35
Alignment explanation
Indices: 1244035--1244156 Score: 142
Period size: 35 Copynumber: 3.5 Consensus size: 35
1244025 ATATGTAAAT
1244035 TATATAGTATATAAATATAAAATATAGTATATATA
1 TATATAGTATATAAATATAAAATATAGTATATATA
*
1244070 TATATAGTATATAAATATAAACTATAGT-T-TATA
1 TATATAGTATATAAATATAAAATATAGTATATATA
* ** * * *
1244103 TAAATAGTATATATTTATAAATTATAGTATGTAGTT
1 TATATAGTATATAAATATAAAATATAGTATATA-TA
*
1244139 TATATA-AATATAAATATA
1 TATATAGTATATAAATATA
1244157 CACCCTAAAC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
33 28 0.38
34 2 0.03
35 38 0.51
36 6 0.08
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.43
Consensus pattern (35 bp):
TATATAGTATATAAATATAAAATATAGTATATATA
Found at i:1244072 original size:33 final size:33
Alignment explanation
Indices: 1244035--1244132 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 33
1244025 ATATGTAAAT
1244035 TATATAGTATATAAATATAAAATATAGTATATATA
1 TATATAGTATATAAATATAAAATATAG--TATATA
* *
1244070 TATATAGTATATAAATATAAACTATAGTTTATA
1 TATATAGTATATAAATATAAAATATAGTATATA
* ** *
1244103 TAAATAGTATATATTTATAAATTATAGTAT
1 TATATAGTATATAAATATAAAATATAGTAT
1244133 GTAGTTTATA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 30 0.54
35 26 0.46
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (33 bp):
TATATAGTATATAAATATAAAATATAGTATATA
Found at i:1244185 original size:14 final size:14
Alignment explanation
Indices: 1244162--1244199 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1244152 ATATACACCC
*
1244162 TAAACTCTAATACT
1 TAAACCCTAATACT
*
1244176 TAAACCCTAATATT
1 TAAACCCTAATACT
1244190 TAAACCCTAA
1 TAAACCCTAA
1244200 ACCATATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAACCCTAATACT
Found at i:1244275 original size:29 final size:31
Alignment explanation
Indices: 1244243--1244300 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
1244233 AGTATATATT
*
1244243 TATAAATTATATTATGTA-GTT-TATATAAA
1 TATAAATTATACTATGTAGGTTCTATATAAA
1244272 TATAAATTATACTATGTAGGTTCTATATA
1 TATAAATTATACTATGTAGGTTCTATATA
1244301 GTTCAATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 17 0.65
30 3 0.12
31 6 0.23
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (31 bp):
TATAAATTATACTATGTAGGTTCTATATAAA
Found at i:1244354 original size:35 final size:33
Alignment explanation
Indices: 1244313--1244438 Score: 120
Period size: 35 Copynumber: 3.8 Consensus size: 33
1244303 TCAATAGTTC
1244313 ATATATA-AACTATATAGTATTATAGTTTATACAT
1 ATATATATAACTATATAGT-TTATA-TTTATACAT
*
1244347 GATATATATAGAC--TATAGTTTATA--CATA-AT
1 -ATATATATA-ACTATATAGTTTATATTTATACAT
*
1244377 ATATATATAAACTATATAGTTTATATATAATACAT
1 ATATATAT-AACTATATAGTTTATAT-TTATACAT
*
1244412 ACTTTATATAACTATATAGTTTATATT
1 A-TATATATAACTATATAGTTTATATT
1244439 ACATATATAT
Statistics
Matches: 78, Mismatches: 3, Indels: 21
0.76 0.03 0.21
Matches are distributed among these distances:
29 10 0.13
30 3 0.04
31 14 0.18
34 9 0.12
35 33 0.42
36 7 0.09
37 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (33 bp):
ATATATATAACTATATAGTTTATATTTATACAT
Found at i:1244369 original size:27 final size:28
Alignment explanation
Indices: 1244295--1244383 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 28
1244285 ATGTAGGTTC
* * * *
1244295 TATATAGTTCAATAGTTCATATATAA-A
1 TATATAGTACTATAGTTTATACATAATA
* *
1244322 CTATATAGTATTATAGTTTATACATGATA
1 -TATATAGTACTATAGTTTATACATAATA
1244351 TATATAG-ACTATAGTTTATACATAATA
1 TATATAGTACTATAGTTTATACATAATA
1244378 TATATA
1 TATATA
1244384 TAAACTATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
27 24 0.46
28 27 0.52
29 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (28 bp):
TATATAGTACTATAGTTTATACATAATA
Found at i:1244395 original size:31 final size:31
Alignment explanation
Indices: 1244333--1244436 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
1244323 TATATAGTAT
* *
1244333 TATAGTTTATACAT--GATATATATAGAC--
1 TATAGTTTATACATAATATATATATAAACTA
1244360 TATAGTTTATACATAATATATATATAAACTA
1 TATAGTTTATACATAATATATATATAAACTA
* *
1244391 TATAGTTTATATATAATACATACTTTATATAACTA
1 TATAGTTTATACATAAT--ATA-TATATA-AACTA
1244426 TATAGTTTATA
1 TATAGTTTATA
1244437 TTACATATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
27 14 0.22
29 11 0.17
31 16 0.25
33 3 0.05
34 5 0.08
35 16 0.25
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (31 bp):
TATAGTTTATACATAATATATATATAAACTA
Found at i:1244448 original size:66 final size:66
Alignment explanation
Indices: 1244313--1244436 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
1244303 TCAATAGTTC
*
1244313 ATATATAAACTATATAGTATTATAGTTTATACATGATATATATAGACTATAGTTTATACATAATA
1 ATATATAAACTATATAGTATTATAGTTAATACATGATATATATAGACTATAGTTTATACATAATA
1244378 T
66 T
*
1244379 ATATATAAACTATATAGT-TTATA-TATAATACAT-ACTTTATATA-ACTATATAGTTTATA
1 ATATATAAACTATATAGTATTATAGT-TAATACATGA-TATATATAGAC--TATAGTTTATA
1244437 TTACATATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
64 4 0.08
65 19 0.37
66 29 0.56
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (66 bp):
ATATATAAACTATATAGTATTATAGTTAATACATGATATATATAGACTATAGTTTATACATAATA
T
Found at i:1245159 original size:218 final size:216
Alignment explanation
Indices: 1244531--1245227 Score: 1029
Period size: 209 Copynumber: 3.3 Consensus size: 216
1244521 TGATCCCTTT
* * *
1244531 TGTGTTGTTTAATTTA-TTAAAGATTTT-TTTGTAATTTCATATTTTTTCAATTTAGTCCTCCAC
1 TGTGTTGTTTAATTTATTTAAA-TTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAA
* *
1244594 ATTTTATTTGCATATGAAATTGACCCATACTTATTACTT-ATTTCTATTTATTAATTGGCCCATA
65 ATTTTATTTGCATATGAAATTGACCCATACTTATTACTTAATTTAT-TTTTTTAATTGGCCCATA
* * *
1244658 ACTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACCTCAAAATTTAAAATTAT
129 ACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTAT
*
1244723 TTCAATTTGATCCCT--T---T-
194 TTCGATTTGATCCCTCATCAATG
* * * *
1244740 TGTGTTGTTTAGTTTATTTAAATTTTTATTTGTTATTTTATATTTTTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* * * **
1244805 -ATTATTTGCATCTGAAATTGACCCATACTTATTACTT-ATTTCTGTTTTAAAATTGGCCCATAA
66 TTTTATTTGCATATGAAATTGACCCATACTTATTACTTAATTTAT-TTTTTTAATTGGCCCATAA
*
1244868 CTTTTTAAATGGATATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
130 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
*
1244933 TTGATTTGATCCCTCATCAATG
195 TCGATTTGATCCCTCATCAATG
* *
1244955 TGTGTTGTTTAATTAATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* * * *
1245020 TTTTATTTGCATATGAAATTGATCCATGCTTTTTACTTAATTATATTTTTTTAATTGGCTCATAA
66 TTTTATTTGCATATGAAATTGACCCATACTTATTACTTAATT-TATTTTTTTAATTGGCCCATAA
*
1245085 CTTTTTAAATGGGTATAATTTAGTACTTTTTTTGTATTAATTTCAATATCACAATTTAAAATTAT
130 CTTTTTAAATGGGTATAATTTAGTAC-TTTTTTGTATTAATTTCAACATCACAATTTAAAATTAT
1245150 TTCGATTTGATCCCTCATCAATG
194 TTCGATTTGATCCCTCATCAATG
1245173 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1245228 ATTCTTAAAT
Statistics
Matches: 440, Mismatches: 36, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
209 149 0.34
210 39 0.09
211 1 0.00
214 1 0.00
215 59 0.13
216 32 0.07
217 44 0.10
218 115 0.26
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (216 bp):
TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
TTTTATTTGCATATGAAATTGACCCATACTTATTACTTAATTTATTTTTTTAATTGGCCCATAAC
TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTT
CGATTTGATCCCTCATCAATG
Found at i:1245925 original size:30 final size:30
Alignment explanation
Indices: 1245882--1245949 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
1245872 TTAAAAATAT
1245882 GTGCCTAATATTTTATCCGTTACACTTTTAG
1 GTGCCT-ATATTTTATCCGTTACACTTTTAG
* *
1245913 GTGCCTATATTTTATTCGTTATACTTTTAG
1 GTGCCTATATTTTATCCGTTACACTTTTAG
*
1245943 GTACCTA
1 GTGCCTA
1245950 CGCAGTAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 28 0.82
31 6 0.18
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (30 bp):
GTGCCTATATTTTATCCGTTACACTTTTAG
Found at i:1253860 original size:7 final size:7
Alignment explanation
Indices: 1253831--1253882 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
1253821 ATTTATAATG
1253831 AACCCTA
1 AACCCTA
1253838 AA-CCTA
1 AACCCTA
*
1253844 AA-CATAA
1 AACCCT-A
1253851 AACCCTA
1 AACCCTA
1253858 AACCCTA
1 AACCCTA
**
1253865 AATACTA
1 AACCCTA
1253872 AACCCTA
1 AACCCTA
1253879 AACC
1 AACC
1253883 TAATTATATG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
6 8 0.22
7 27 0.73
8 2 0.05
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (7 bp):
AACCCTA
Found at i:1253866 original size:21 final size:21
Alignment explanation
Indices: 1253831--1253882 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1253821 ATTTATAATG
1253831 AACCCTAAA-CCTAAACA-TAA
1 AACCCTAAACCCTAAACACT-A
*
1253851 AACCCTAAACCCTAAATACTA
1 AACCCTAAACCCTAAACACTA
1253872 AACCCTAAACC
1 AACCCTAAACC
1253883 TAATTATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.31
21 19 0.66
22 1 0.03
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (21 bp):
AACCCTAAACCCTAAACACTA
Found at i:1254908 original size:27 final size:27
Alignment explanation
Indices: 1254877--1254932 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1254867 TATATACACC
1254877 TCTGCTATTTCGTTGGTCAATGAAGCA
1 TCTGCTATTTCGTTGGTCAATGAAGCA
1254904 TCTGCTATTTCGTTGGTCAATGAAGCA
1 TCTGCTATTTCGTTGGTCAATGAAGCA
1254931 TC
1 TC
1254933 CCAATCATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (27 bp):
TCTGCTATTTCGTTGGTCAATGAAGCA
Found at i:1256530 original size:24 final size:24
Alignment explanation
Indices: 1256472--1256562 Score: 139
Period size: 24 Copynumber: 3.8 Consensus size: 24
1256462 TTAACCCCAC
* * *
1256472 CTCGAGCTTGAATCGAGCTCAAAT
1 CTCGAGCTTCAATCGAGCTCGAGT
*
1256496 -TTGAGCTTCAATCGAGCTCGAGT
1 CTCGAGCTTCAATCGAGCTCGAGT
1256519 CTCGAGCTTCAATCGAGCTCGAGT
1 CTCGAGCTTCAATCGAGCTCGAGT
1256543 CTCGAGCTTCAATCGAGCTC
1 CTCGAGCTTCAATCGAGCTC
1256563 CTGAAATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.31
24 42 0.69
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (24 bp):
CTCGAGCTTCAATCGAGCTCGAGT
Found at i:1259236 original size:21 final size:21
Alignment explanation
Indices: 1259179--1259284 Score: 53
Period size: 21 Copynumber: 5.3 Consensus size: 21
1259169 TATAATAAAA
** *
1259179 TATTAATTATAATAATTAAAT
1 TATTAATTATAATTCTTATAT
* * *
1259200 TAATAAATAT-A-T-TTATTT
1 TATTAATTATAATTCTTATAT
1259218 TATTAATTATAATTCTTATAT
1 TATTAATTATAATTCTTATAT
* * * *
1259239 TATGATTTATAAATCTT-TAA
1 TATTAATTATAATTCTTATAT
* *
1259259 TA-TAATCATTAATT-TTATTT
1 TATTAATTA-TAATTCTTATAT
1259279 TATTAA
1 TATTAA
1259285 GTAATTTATG
Statistics
Matches: 61, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
18 12 0.20
19 6 0.10
20 13 0.21
21 30 0.49
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (21 bp):
TATTAATTATAATTCTTATAT
Found at i:1259417 original size:18 final size:18
Alignment explanation
Indices: 1259394--1259496 Score: 124
Period size: 18 Copynumber: 5.9 Consensus size: 18
1259384 ATTAATGAAT
*
1259394 TATATAATATATAGTTTA
1 TATATACTATATAGTTTA
*
1259412 TATATACTATATAATTTA
1 TATATACTATATAGTTTA
*
1259430 TATATACTA-AT-G--AA
1 TATATACTATATAGTTTA
*
1259444 CTATATAATATATAGTTTA
1 -TATATACTATATAGTTTA
*
1259463 TATATACCATATAGTTTA
1 TATATACTATATAGTTTA
1259481 TATATACTATATAGTT
1 TATATACTATATAGTT
1259497 AGAATAAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
14 1 0.01
15 8 0.11
16 2 0.03
17 3 0.04
18 56 0.79
19 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.47
Consensus pattern (18 bp):
TATATACTATATAGTTTA
Found at i:1259449 original size:51 final size:51
Alignment explanation
Indices: 1259386--1259489 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
1259376 CATTTAAAAT
* *
1259386 TAATGAATTATATAATATATAGTTTATATATACTATATAATTTATATATAC
1 TAATGAACTATATAATATATAGTTTATATATACCATATAATTTATATATAC
*
1259437 TAATGAACTATATAATATATAGTTTATATATACCATATAGTTTATATATAC
1 TAATGAACTATATAATATATAGTTTATATATACCATATAATTTATATATAC
1259488 TA
1 TA
1259490 TATAGTTAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (51 bp):
TAATGAACTATATAATATATAGTTTATATATACCATATAATTTATATATAC
Found at i:1261300 original size:18 final size:18
Alignment explanation
Indices: 1261247--1261608 Score: 324
Period size: 18 Copynumber: 21.2 Consensus size: 18
1261237 ATTATTAATT
1261247 TATACTAT-TAGTTTATA
1 TATACTATATAGTTTATA
*
1261264 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
*
1261279 TATAATATATAGTTTATA
1 TATACTATATAGTTTATA
1261297 TATACTATATAGTTTATA
1 TATACTATATAGTTTATA
*
1261315 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
* *
1261330 TATAATATATAGTTTGTA
1 TATACTATATAGTTTATA
*
1261348 TATACCATATAGTTTATA
1 TATACTATATAGTTTATA
1261366 TAT--TATATAGTTTATA
1 TATACTATATAGTTTATA
*
1261382 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
* * *
1261397 TATAATATGTAGTTTTTA
1 TATACTATATAGTTTATA
*
1261415 TATACCATATAGTTTATA
1 TATACTATATAGTTTATA
*
1261433 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
*
1261448 TATAATATATAGTTTATA
1 TATACTATATAGTTTATA
*
1261466 TATACCATATAGTTTATA
1 TATACTATATAGTTTATA
*
1261484 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
* *
1261499 TATAATATATAATTTATA
1 TATACTATATAGTTTATA
*
1261517 TATACTATATAGTTTATG
1 TATACTATATAGTTTATA
1261535 TATACTATATAG-TT-TA
1 TATACTATATAGTTTATA
1261551 TATACTATATAGTTTATA
1 TATACTATATAGTTTATA
*
1261569 TAAACTATATAGTTTATA
1 TATACTATATAGTTTATA
*
1261587 TAAACTATATAGTTTATA
1 TATACTATATAGTTTATA
1261605 TATA
1 TATA
1261609 TACGCTAAAT
Statistics
Matches: 277, Mismatches: 38, Indels: 59
0.74 0.10 0.16
Matches are distributed among these distances:
14 5 0.02
15 40 0.14
16 42 0.15
17 24 0.09
18 163 0.59
19 3 0.01
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
TATACTATATAGTTTATA
Found at i:1261316 original size:51 final size:51
Alignment explanation
Indices: 1261247--1261368 Score: 219
Period size: 51 Copynumber: 2.4 Consensus size: 51
1261237 ATTATTAATT
1261247 TATACTAT-TAGTTTATATATACTAATGAACTATATAATATATAGTTTATA
1 TATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATA
*
1261297 TATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTA
1 TATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATA
*
1261348 TATACCATATAGTTTATATAT
1 TATACTATATAGTTTATATAT
1261369 TATATAGTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
50 8 0.12
51 61 0.88
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (51 bp):
TATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATA
Found at i:1261383 original size:67 final size:68
Alignment explanation
Indices: 1261285--1261436 Score: 270
Period size: 67 Copynumber: 2.2 Consensus size: 68
1261275 ACTATATAAT
1261285 ATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATA
1 ATATAGTTTATATATA-TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATA
1261350 TACC
65 TACC
* *
1261354 ATATAGTTTATATAT-TATATAGTTTATATATACTAATGAACTATATAATATGTAGTTTTTATAT
1 ATATAGTTTATATATATATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATAT
1261418 ACC
66 ACC
1261421 ATATAGTTTATATATA
1 ATATAGTTTATATATA
1261437 CTAATGAACT
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
67 65 0.81
69 15 0.19
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (68 bp):
ATATAGTTTATATATATATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATAT
ACC
Found at i:1261385 original size:118 final size:118
Alignment explanation
Indices: 1261247--1261607 Score: 457
Period size: 118 Copynumber: 3.0 Consensus size: 118
1261237 ATTATTAATT
*
1261247 TATACTAT-TAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATATAGTT
1 TATATTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATATAGTT
*
1261311 TATATATACTAATGAACTATATAATATATAGTTTGTATATACCATATAGTTTA
66 TATATATACTAATGAACTATATAATATATAGTTTATATATACCATATAGTTTA
* * *
1261364 TATATTATATAGTTTATATATACTAATGAACTATATAATATGTAGTTTTTATATACCATATAGTT
1 TATATTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATATAGTT
1261429 TATATATACTAATGAACTATATAATATATAGTTTATATATACCATATAGTTTA
66 TATATATACTAATGAACTATATAATATATAGTTTATATATACCATATAGTTTA
* * ** * *
1261482 TATA-TACTAATGAACTATATAATATA-TAATTTA-TATATACTATATAGTTTATGTATACTATA
1 TATATTA-T-AT--AGTTTAT-ATATACTAATGAACTATATAATATATAGTTTATATATACTATA
** * *
1261544 TAG-TT-TATATACTATAT-AGTTTATATAAACTATATAGTTTATATAAACTATATAGTTTA
61 TAGTTTATATATACTA-ATGA-ACTATAT-AA-TATATAGTTTATATATACCATATAGTTTA
1261603 TATAT
1 TATAT
1261608 ATACGCTAAA
Statistics
Matches: 215, Mismatches: 18, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
117 9 0.04
118 120 0.56
119 11 0.05
120 29 0.13
121 41 0.19
122 5 0.02
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (118 bp):
TATATTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATATAGTT
TATATATACTAATGAACTATATAATATATAGTTTATATATACCATATAGTTTA
Found at i:1261415 original size:51 final size:51
Alignment explanation
Indices: 1261354--1261593 Score: 342
Period size: 51 Copynumber: 4.7 Consensus size: 51
1261344 TGTATATACC
1261354 ATATAGTTTATATAT--TATATAGTTTATATATACTAATGAACTATATAAT
1 ATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATATAAT
* * *
1261403 ATGTAGTTTTTATATACCATATAGTTTATATATACTAATGAACTATATAAT
1 ATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATATAAT
*
1261454 ATATAGTTTATATATACCATATAGTTTATATATACTAATGAACTATATAAT
1 ATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATATAAT
* * ** *
1261505 ATATAATTTATATATACTATATAGTTTATGTATACTATAT-AGTTTATATACT
1 ATATAGTTTATATATACTATATAGTTTATATATACTA-ATGA-ACTATATAAT
* *
1261557 ATATAGTTTATATAAACTATATAGTTTATATAAACTA
1 ATATAGTTTATATATACTATATAGTTTATATATACTA
1261594 TATAGTTTAT
Statistics
Matches: 172, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
49 13 0.08
51 117 0.68
52 42 0.24
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (51 bp):
ATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATATAAT
Found at i:1261628 original size:18 final size:18
Alignment explanation
Indices: 1261284--1261699 Score: 245
Period size: 18 Copynumber: 23.8 Consensus size: 18
1261274 AACTATATAA
*
1261284 TATATAGTTTATATATAC
1 TATATAGTTTATATAAAC
*
1261302 TATATAGTTTATATATAC
1 TATATAGTTTATATAAAC
**
1261320 TA-AT-GAACTATAT-AA-
1 TATATAG-TTTATATAAAC
* *
1261335 TATATAGTTTGTATATAC
1 TATATAGTTTATATAAAC
* *
1261353 CATATAGTTTATAT--AT
1 TATATAGTTTATATAAAC
*
1261369 TATATAGTTTATATATAC
1 TATATAGTTTATATAAAC
**
1261387 TA-AT-GAACTATAT-AA-
1 TATATAG-TTTATATAAAC
* * *
1261402 TATGTAGTTTTTATATAC
1 TATATAGTTTATATAAAC
* *
1261420 CATATAGTTTATATATAC
1 TATATAGTTTATATAAAC
**
1261438 TA-AT-GAACTATAT-AA-
1 TATATAG-TTTATATAAAC
*
1261453 TATATAGTTTATATATAC
1 TATATAGTTTATATAAAC
* *
1261471 CATATAGTTTATATATAC
1 TATATAGTTTATATAAAC
**
1261489 TA-AT-GAACTATAT-AA-
1 TATATAG-TTTATATAAAC
* *
1261504 TATATAATTTATATATAC
1 TATATAGTTTATATAAAC
* *
1261522 TATATAGTTTATGTATAC
1 TATATAGTTTATATAAAC
1261540 TATATAGTTTATAT--AC
1 TATATAGTTTATATAAAC
1261556 TATATAGTTTATATAAAC
1 TATATAGTTTATATAAAC
1261574 TATATAGTTTATATAAAC
1 TATATAGTTTATATAAAC
1261592 TATATAGTTTATATATATACGC
1 TATATAGTTTATATA-A-A--C
*
1261614 TAAATAGTTTATATACAA-
1 TATATAGTTTATATA-AAC
* *
1261632 TATAAAATTATAAATATAAAC
1 TATATAGTT-T--ATATAAAC
**
1261653 TATATACATTATATAAAAC
1 TATATAGTTTATAT-AAAC
1261672 TATA-A----ATATAAAC
1 TATATAGTTTATATAAAC
1261685 TATATAGTTTATATA
1 TATATAGTTTATATA
1261700 TGTTATATAT
Statistics
Matches: 310, Mismatches: 50, Indels: 76
0.71 0.11 0.17
Matches are distributed among these distances:
13 8 0.03
14 5 0.02
15 8 0.03
16 63 0.20
17 35 0.11
18 149 0.48
19 10 0.03
20 4 0.01
21 12 0.04
22 16 0.05
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (18 bp):
TATATAGTTTATATAAAC
Found at i:1261676 original size:32 final size:32
Alignment explanation
Indices: 1261623--1261699 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
1261613 CTAAATAGTT
*
1261623 TATATACA--ATATAAAATTATAAATATAAAC
1 TATATACATTATATAAAACTATAAATATAAAC
1261653 TATATACATTATATAAAACTATAAATATAAAC
1 TATATACATTATATAAAACTATAAATATAAAC
**
1261685 TATATAGTTTATATA
1 TATATACATTATATA
1261700 TGTTATATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
30 8 0.19
32 34 0.81
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (32 bp):
TATATACATTATATAAAACTATAAATATAAAC
Found at i:1261714 original size:15 final size:17
Alignment explanation
Indices: 1261693--1261732 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
1261683 ACTATATAGT
*
1261693 TTATATATGTT-ATATA
1 TTATATATATTAATATA
1261709 -TATATATATTAATATA
1 TTATATATATTAATATA
1261725 TTATATAT
1 TTATATAT
1261733 TTTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTATATATATTAATATA
Found at i:1263384 original size:108 final size:107
Alignment explanation
Indices: 1263248--1263757 Score: 595
Period size: 108 Copynumber: 4.8 Consensus size: 107
1263238 TATTAATACG
* * ** * * *
1263248 AGGTTGCACCTAATATGTTATGAGAGTTTAAGTTGATGGAGCCTTAGAAATCTCTCGATAACAAA
1 AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAGCCTTAGAAATCTCACGATAACAAA
*
1263313 ATAGTTTAATTACTTATTTTATTATAAATATTATTAACATAAT
66 ATAG-TTAATTACTTATTTTATTATAAATATTATTAACATATT
* *
1263356 AGGTTACACGTAAAATGTTAACAAAGTTTAAGCTGATGGAGGCTTAGAAAT-TCTACGATAA-AA
1 AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAGCCTTAGAAATCTC-ACGATAACAA
*
1263419 AAAAGTTAATTACTTATTTTATTATAAATATTATTAACATATT
65 AATAGTTAATTACTTATTTTATTATAAATATTATTAACATATT
* * * * *
1263462 AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGAT-GAGACATTAGAAATCTCAC-AGTAACA
1 AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAG-CCTTAGAAATCTCACGA-TAACA
* *
1263525 AAATAAG-TAATTAACTTATTTTGTTATAAATTTTATTAACATATT
64 AAAT-AGTTAATT-ACTTATTTTATTATAAATATTATTAACATATT
** * * * * *
1263570 AAATTGCGCCTAAAATGTTAACAGAGATTAAGCTGATGGGGCCTTAGAAATCTCACGATAAC-AA
1 AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAGCCTTAGAAATCTCACGATAACAAA
*
1263634 A-AGTTAATTACTTATTTTGTTATAAATATTATTAACATATT
66 ATAGTTAATTACTTATTTTATTATAAATATTATTAACATATT
* * * *
1263675 AGGCTACACCTAAAATGTTACCAAAGTTTAAGCTAATGGGGCCTTAGATAATC-CAACGATAACA
1 AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAGCCTTAGA-AATCTC-ACGATAACA
* *
1263739 AAATAAATTAATTATTTAT
64 AAAT-AGTTAATTACTTAT
1263758 AATGTTATGA
Statistics
Matches: 344, Mismatches: 43, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
105 77 0.22
106 99 0.29
107 25 0.07
108 128 0.37
109 15 0.04
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (107 bp):
AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAGCCTTAGAAATCTCACGATAACAAA
ATAGTTAATTACTTATTTTATTATAAATATTATTAACATATT
Found at i:1263618 original size:214 final size:212
Alignment explanation
Indices: 1263248--1263757 Score: 618
Period size: 214 Copynumber: 2.4 Consensus size: 212
1263238 TATTAATACG
* ** * * * * *
1263248 AGGTTGCACCTAATATGTTATGAGAGTTTAAGTTGATGGAGCCTTAGAAATCTCTCGATAACAAA
1 AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGATGGAGCATTAGAAATCTCACGATAACAAA
** *
1263313 ATAGTTTAATTACTTATTTTATTATAAATATTATTAACATAATAGGTTACACGTAAAATGTTAAC
66 ATAG-TTAATTACTTATTTTATTATAAATATTATTAACATAATAAATTACACCTAAAATGTTAAC
*
1263378 AAAGTTTAAGCTGATGGAGGCTTAGAAAT-TCTACGATAAAAAAAAGTTAATTACTTATTTTATT
130 AAAGATTAAGCTGATGGAGGCTTAGAAATCTC-ACGAT-AAAAAAAGTTAATTACTTATTTTATT
1263442 ATAAATATTATTAACATATT
193 ATAAATATTATTAACATATT
1263462 AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGAT-GAGACATTAGAAATCTCAC-AGTAACA
1 AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGATGGAG-CATTAGAAATCTCACGA-TAACA
* * * * *
1263525 AAATAAG-TAATTAACTTATTTTGTTATAAATTTTATTAACATATTAAATTGCGCCTAAAATGTT
64 AAAT-AGTTAATT-ACTTATTTTATTATAAATATTATTAACATAATAAATTACACCTAAAATGTT
* * *
1263589 AACAGAGATTAAGCTGATGG-GGCCTTAGAAATCTCACGATAACAAAAGTTAATTACTTATTTTG
127 AACAAAGATTAAGCTGATGGAGG-CTTAGAAATCTCACGATAAAAAAAGTTAATTACTTATTTTA
1263653 TTATAAATATTATTAACATATT
191 TTATAAATATTATTAACATATT
* * * * * * *
1263675 AGGCTACACCTAAAATGTTACCAAAGTTTAAGCTAATGGGGCCTTAGATAATC-CAACGATAACA
1 AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGATGGAGCATTAGA-AATCTC-ACGATAACA
* *
1263739 AAATAAATTAATTATTTAT
64 AAAT-AGTTAATTACTTAT
1263758 AATGTTATGA
Statistics
Matches: 256, Mismatches: 29, Indels: 22
0.83 0.09 0.07
Matches are distributed among these distances:
213 94 0.37
214 152 0.59
215 10 0.04
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (212 bp):
AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGATGGAGCATTAGAAATCTCACGATAACAAA
ATAGTTAATTACTTATTTTATTATAAATATTATTAACATAATAAATTACACCTAAAATGTTAACA
AAGATTAAGCTGATGGAGGCTTAGAAATCTCACGATAAAAAAAGTTAATTACTTATTTTATTATA
AATATTATTAACATATT
Found at i:1270187 original size:18 final size:19
Alignment explanation
Indices: 1270164--1270201 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1270154 CTGAAATATG
*
1270164 CCTTGA-AGTATCGATACT
1 CCTTGAGAGTACCGATACT
1270182 CCTTGAGGAGTACCGATACT
1 CCTTGA-GAGTACCGATACT
1270202 ACTCATCGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (19 bp):
CCTTGAGAGTACCGATACT
Found at i:1275504 original size:23 final size:23
Alignment explanation
Indices: 1275450--1275504 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
1275440 TCGAGGGTTT
* * *
1275450 TACGCGATCCTTCGGGATAAATC
1 TACGCGGTCATTCGAGATAAATC
* * *
1275473 TATGTGGTCATTCGAGATAATTC
1 TACGCGGTCATTCGAGATAAATC
1275496 TACGCGGTC
1 TACGCGGTC
1275505 CTTTGGGAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (23 bp):
TACGCGGTCATTCGAGATAAATC
Found at i:1275555 original size:23 final size:24
Alignment explanation
Indices: 1275491--1275589 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 24
1275481 CATTCGAGAT
* * *
1275491 AATTCTACGCGGTC-CTTTGGGAAA
1 AATTCTACGCGG-CACTTCGGTACA
*
1275515 AATTCTACGCAGTC-CTTCAGG-ACA
1 AATTCTACGC-GGCACTTC-GGTACA
* *
1275539 AA-TCTACGTGGCACTTCGGTGCA
1 AATTCTACGCGGCACTTCGGTACA
*
1275562 AATTCTACGCGGCACTTCGGTGCA
1 AATTCTACGCGGCACTTCGGTACA
1275586 AATT
1 AATT
1275590 ATATGAGCAG
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.06
23 14 0.22
24 42 0.67
25 3 0.05
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (24 bp):
AATTCTACGCGGCACTTCGGTACA
Found at i:1275575 original size:24 final size:24
Alignment explanation
Indices: 1275537--1275589 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1275527 TCCTTCAGGA
*
1275537 CAAA-TCTACGTGGCACTTCGGTG
1 CAAATTCTACGCGGCACTTCGGTG
1275560 CAAATTCTACGCGGCACTTCGGTG
1 CAAATTCTACGCGGCACTTCGGTG
1275584 CAAATT
1 CAAATT
1275590 ATATGAGCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (24 bp):
CAAATTCTACGCGGCACTTCGGTG
Found at i:1275715 original size:19 final size:18
Alignment explanation
Indices: 1275669--1275716 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1275659 TACGTTGGGC
*
1275669 TAATTAAATAAATGGATA
1 TAATTAAACAAATGGATA
*
1275687 TAATTAAACAAATTGATA
1 TAATTAAACAAATGGATA
*
1275705 TGAATTGAACAA
1 T-AATTAAACAA
1275717 TAATTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.31
Consensus pattern (18 bp):
TAATTAAACAAATGGATA
Found at i:1280719 original size:21 final size:22
Alignment explanation
Indices: 1280695--1280754 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
1280685 TTCTATGCGA
**
1280695 TCATTCGGGA-AAATTATGTGG
1 TCATTCGGGACAAATTACATGG
*
1280716 TCATTCGGGACAATTCTACATGG
1 TCATTCGGGACAAAT-TACATGG
1280739 TCATTCGGGACAAATT
1 TCATTCGGGACAAATT
1280755 CTACGCGGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.30
22 4 0.12
23 19 0.58
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (22 bp):
TCATTCGGGACAAATTACATGG
Found at i:1280743 original size:23 final size:23
Alignment explanation
Indices: 1280713--1280782 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
1280703 GAAAATTATG
1280713 TGGTCATTCGGGACAATTCTACA
1 TGGTCATTCGGGACAATTCTACA
*
1280736 TGGTCATTCGGGACAAATTCTACG
1 TGGTCATTCGGGAC-AATTCTACA
* * * *
1280760 CGGTCCTTCGAGACAAATCTACA
1 TGGTCATTCGGGACAATTCTACA
1280783 CGCCACTTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (23 bp):
TGGTCATTCGGGACAATTCTACA
Found at i:1280764 original size:24 final size:24
Alignment explanation
Indices: 1280685--1280781 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
1280675 GAGTCGAGGG
* *
1280685 TTCTATGCGATCATTCGGGA-AAA
1 TTCTACGCGGTCATTCGGGACAAA
* *
1280708 -T-TATGTGGTCATTCGGGAC-AA
1 TTCTACGCGGTCATTCGGGACAAA
**
1280729 TTCTACATGGTCATTCGGGACAAA
1 TTCTACGCGGTCATTCGGGACAAA
* *
1280753 TTCTACGCGGTCCTTCGAGACAAA
1 TTCTACGCGGTCATTCGGGACAAA
1280777 -TCTAC
1 TTCTAC
1280782 ACGCCACTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
21 17 0.27
22 2 0.03
23 21 0.34
24 22 0.35
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (24 bp):
TTCTACGCGGTCATTCGGGACAAA
Found at i:1281698 original size:54 final size:54
Alignment explanation
Indices: 1281636--1282018 Score: 355
Period size: 54 Copynumber: 7.1 Consensus size: 54
1281626 AACCGATAAT
** * *
1281636 GTTACTCCTACTTATAAGGTAATTAGTTGAAAATAACAAGGTACAACCATTAAC
1 GTTACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGGTGCAACCATTAAC
* * * *
1281690 GTTACTCCTACTTATAAGGTAA-CGGTTAAAAACAAAACAAGGTGCAACCGTAAAC
1 GTTACTCCTACTTATAAGGTAACCAGTT-AAAA-ATAACAAGGTGCAACCATTAAC
* ***
1281745 GTTACTCCAACTTATAAGGTAACCAGTT-AAAATAACAAGACACAACCATTAAC
1 GTTACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGGTGCAACCATTAAC
* * * *
1281798 ATTACTCCTACTTATAAGGTAACCTA-TTAAAAATAACAAGGCGTAACTATTAAC
1 GTTACTCCTACTTATAAGGTAACC-AGTTAAAAATAACAAGGTGCAACCATTAAC
* ** * ** *
1281852 GTTACTCCTACATATAAGGTAA-TTGATTAAAAATAACAAGATGCAACTGTTAAT
1 GTTACTCCTACTTATAAGGTAACCAG-TTAAAAATAACAAGGTGCAACCATTAAC
* * * * * * * ** * *
1281906 GTTACTCTTACTTACAAAGTTACCCGTTAAAAA-AATAAGGCGCAACTGTAAAT
1 GTTACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGGTGCAACCATTAAC
* *
1281959 GTTACTCCTACTTATAAGGTAATCGGTTAAAAATAACAAGGTGCAACC-TATAAC
1 GTTACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGGTGCAACCAT-TAAC
1282013 GTTACT
1 GTTACT
1282019 AAAAAATGTT
Statistics
Matches: 267, Mismatches: 52, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
53 87 0.33
54 136 0.51
55 40 0.15
56 4 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (54 bp):
GTTACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGGTGCAACCATTAAC
Found at i:1281817 original size:108 final size:109
Alignment explanation
Indices: 1281582--1281820 Score: 315
Period size: 109 Copynumber: 2.2 Consensus size: 109
1281572 CATTAAGGTT
* * *
1281582 TTACTCCCT-CTTATAAGG-AACCGATAAAAAACAAAACATGACGCAACCGATAATGTTACTCCT
1 TTACT-CCTACTTATAAGGTAA-CGATAAAAAACAAAACAAGACGCAACCGATAACGTTACTCCA
** ** *
1281645 ACTTATAAGGTAATTAGTTGAAAATAACAAGGTACAACCATTAACG
64 ACTTATAAGGTAACCAGTTGAAAATAACAAGACACAACCATTAACA
* * **
1281691 TTACTCCTACTTATAAGGTAACGGTTAAAAACAAAACAAGGTGCAACCG-TAAACGTTACTCCAA
1 TTACTCCTACTTATAAGGTAACGATAAAAAACAAAACAAGACGCAACCGAT-AACGTTACTCCAA
1281755 CTTATAAGGTAACCAGTT-AAAATAACAAGACACAACCATTAACA
65 CTTATAAGGTAACCAGTTGAAAATAACAAGACACAACCATTAACA
1281799 TTACTCCTACTTATAAGGTAAC
1 TTACTCCTACTTATAAGGTAAC
1281821 CTATTAAAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
108 49 0.43
109 64 0.56
110 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (109 bp):
TTACTCCTACTTATAAGGTAACGATAAAAAACAAAACAAGACGCAACCGATAACGTTACTCCAAC
TTATAAGGTAACCAGTTGAAAATAACAAGACACAACCATTAACA
Found at i:1281885 original size:108 final size:107
Alignment explanation
Indices: 1281636--1282018 Score: 400
Period size: 107 Copynumber: 3.6 Consensus size: 107
1281626 AACCGATAAT
* * *
1281636 GTTACTCCTACTTATAAGGTAAT-TAGTTGAAAATAACAAGGTACAACCATTAACGTTACTCCTA
1 GTTACTCCTACTTATAAGGTAATCGAGTTAAAAATAACAAGATACAACCATTAACGTTACTCCTA
* * * *
1281700 CTTATAAGGTAACGGTTAAAAACAAAACAAGGTGCAACCGTAAAC
66 CTTATAAGGTAAC-CTT-TAAA-AAAACAAGGCGCAACTGTAAAC
* * * *
1281745 GTTACTCCAACTTATAAGGTAA-CCAGTT-AAAATAACAAGACACAACCATTAACATTACTCCTA
1 GTTACTCCTACTTATAAGGTAATCGAGTTAAAAATAACAAGATACAACCATTAACGTTACTCCTA
* * *
1281808 CTTATAAGGTAACCTATTAAAAATAACAAGGCGTAACTATTAAC
66 CTTATAAGGTAACCT-TTAAAAA-AACAAGGCGCAACTGTAAAC
* * * ** * *
1281852 GTTACTCCTACATATAAGGTAATTGA-TTAAAAATAACAAGATGCAACTGTTAATGTTACTCTTA
1 GTTACTCCTACTTATAAGGTAATCGAGTTAAAAATAACAAGATACAACCATTAACGTTACTCCTA
* * * * * *
1281916 CTTACAAAGTTACCCGTTAAAAAAATAAGGCGCAACTGTAAAT
66 CTTA-TAAGGTAACCTTTAAAAAAACAAGGCGCAACTGTAAAC
* *
1281959 GTTACTCCTACTTATAAGGTAATCG-GTTAAAAATAACAAGGTGCAACC-TATAACGTTACT
1 GTTACTCCTACTTATAAGGTAATCGAGTTAAAAATAACAAGATACAACCAT-TAACGTTACT
1282019 AAAAAATGTT
Statistics
Matches: 229, Mismatches: 37, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
106 3 0.01
107 108 0.47
108 86 0.38
109 32 0.14
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (107 bp):
GTTACTCCTACTTATAAGGTAATCGAGTTAAAAATAACAAGATACAACCATTAACGTTACTCCTA
CTTATAAGGTAACCTTTAAAAAAACAAGGCGCAACTGTAAAC
Found at i:1281991 original size:161 final size:162
Alignment explanation
Indices: 1281614--1282018 Score: 442
Period size: 161 Copynumber: 2.5 Consensus size: 162
1281604 GATAAAAAAC
* * * *
1281614 AAAACATGACGCAACCGAT-AATGTTACTCCTACTTATAAGGTAATTAGTTGAAAATAACAAGGT
1 AAAACAAGACACAACC-ATAAATGTTACTCCTACTTATAAGGTAATCAGTTAAAAATAACAAGGT
* * * * *
1281678 ACAACCATTAACGTTACTCCTACTTATAAGGTAACGGTTAAAAACAAAACAAGGTGCAACCGTAA
65 GCAACTATTAACGTTACTCCTACATATAAGGTAACGATTAAAAACAAAACAAGATGCAACCGTAA
* *
1281743 ACGTTACTCCAACTTATAAGGTAACCAGTTAAA
130 ACGTTACTCCAACTTACAAAGTAACCAGTTAAA
* * ** * *
1281776 ATAACAAGACACAACCATTAACATTACTCCTACTTATAAGGTAACCTA-TTAAAAATAACAAGGC
1 AAAACAAGACACAACCATAAATGTTACTCCTACTTATAAGGTAATC-AGTTAAAAATAACAAGGT
* * * * *
1281840 GTAACTATTAACGTTACTCCTACATATAAGGTAATTGATT-AAAA-ATAACAAGATGCAACTGTT
65 GCAACTATTAACGTTACTCCTACATATAAGGTAA-CGATTAAAAACAAAACAAGATGCAACCGTA
* ** * *
1281903 AATGTTACTCTTACTTACAAAGTTACCCGTTAAA
129 AACGTTACTCCAACTTACAAAGTAACCAGTTAAA
* * * ** *
1281937 AAAATAAGGCGCAACTGTAAATGTTACTCCTACTTATAAGGTAATCGGTTAAAAATAACAAGGTG
1 AAAACAAGACACAACCATAAATGTTACTCCTACTTATAAGGTAATCAGTTAAAAATAACAAGGTG
1282002 CAACCTA-TAACGTTACT
66 CAA-CTATTAACGTTACT
1282019 AAAAAATGTT
Statistics
Matches: 199, Mismatches: 39, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
161 108 0.54
162 87 0.44
163 4 0.02
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.27
Consensus pattern (162 bp):
AAAACAAGACACAACCATAAATGTTACTCCTACTTATAAGGTAATCAGTTAAAAATAACAAGGTG
CAACTATTAACGTTACTCCTACATATAAGGTAACGATTAAAAACAAAACAAGATGCAACCGTAAA
CGTTACTCCAACTTACAAAGTAACCAGTTAAA
Found at i:1282119 original size:19 final size:19
Alignment explanation
Indices: 1282086--1282157 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
1282076 AATACAAAGT
1282086 ATCGAAACTTTGTTATGAAG
1 ATCGAAAC-TTGTTATGAAG
1282106 ATCGAAACTTGTTATG-AG
1 ATCGAAACTTGTTATGAAG
*
1282124 AATCAAAACTTGTTAT-AAGG
1 -ATCGAAACTTGTTATGAA-G
*
1282144 ATCGAAGCTTGTTA
1 ATCGAAACTTGTTA
1282158 AAAATAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 2 0.04
19 35 0.76
20 9 0.20
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (19 bp):
ATCGAAACTTGTTATGAAG
Found at i:1282391 original size:51 final size:52
Alignment explanation
Indices: 1282276--1282393 Score: 143
Period size: 51 Copynumber: 2.3 Consensus size: 52
1282266 ACTTTGCGAA
* *
1282276 AAAGT-TCAATACTTTGCAGCCTTTCATTTTCTATGTTTTTTTTTTAAATTCG
1 AAAGTATCAATACTTTACAGCCTTTCATTTTCCATG-TTTTTTTTTAAATTCG
* * * *
1282328 AAAGTATTAATACTTTACATCCTTCTCGTTTTCCATG-TTTTTTTT-AATTTG
1 AAAGTATCAATACTTTACAGCCTT-TCATTTTCCATGTTTTTTTTTAAATTCG
1282379 AAAGTATCAATACTT
1 AAAGTATCAATACTT
1282394 GTGAAAAGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
51 19 0.33
52 13 0.23
53 15 0.26
54 10 0.18
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.50
Consensus pattern (52 bp):
AAAGTATCAATACTTTACAGCCTTTCATTTTCCATGTTTTTTTTTAAATTCG
Found at i:1283144 original size:2 final size:2
Alignment explanation
Indices: 1283137--1283201 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1283127 TTATTGTAGC
1283137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1283179 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1283202 TTATTGAGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.