Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005083.1 Hibiscus syriacus cultivar Beakdansim tig00011417_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: 344126
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:234953 original size:20 final size:20
Alignment explanation
Indices: 234928--234979 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
234918 TCTGTGATCA
*
234928 ATGGTATCGATAC-CATCCTC
1 ATGGTATCGATACTC-CCCTC
*
234948 ATGGTATCAATACTCCCCTC
1 ATGGTATCGATACTCCCCTC
*
234968 TTGGTATCGATA
1 ATGGTATCGATA
234980 ACACTTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGGTATCGATACTCCCCTC
Found at i:236610 original size:22 final size:22
Alignment explanation
Indices: 236585--236628 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
236575 AAATTTTATA
** *
236585 AAAATATTTAATTTTAAAATAT
1 AAAATATGAAATTATAAAATAT
236607 AAAATATGAAATTATAAAATAT
1 AAAATATGAAATTATAAAATAT
236629 CATCACCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATATGAAATTATAAAATAT
Found at i:236756 original size:19 final size:19
Alignment explanation
Indices: 236714--236756 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
236704 AATTTAATAT
* * *
236714 ATATTTATATATATATAAT
1 ATATTTAGATATAAATAAA
*
236733 GTATTTAGATATAAATAAA
1 ATATTTAGATATAAATAAA
236752 ATATT
1 ATATT
236757 AGAATTTTTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
ATATTTAGATATAAATAAA
Found at i:238810 original size:21 final size:21
Alignment explanation
Indices: 238786--238831 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
238776 AATAACCATT
*
238786 GGATCAATTCACTACACAATA
1 GGATCAATTCACTACACAACA
238807 GGATCAATTCACTACACAACA
1 GGATCAATTCACTACACAACA
238828 GGAT
1 GGAT
238832 GAATCCCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (21 bp):
GGATCAATTCACTACACAACA
Found at i:238929 original size:21 final size:21
Alignment explanation
Indices: 238905--238954 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
238895 AAAAAAGAAT
238905 GATCCCTTCTC-TCGAAGGATC
1 GATCCCTTC-CATCGAAGGATC
238926 GATCCCTTCCATCGAAGGATC
1 GATCCCTTCCATCGAAGGATC
238947 GATCCCTT
1 GATCCCTT
238955 GATTGATCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (21 bp):
GATCCCTTCCATCGAAGGATC
Found at i:240273 original size:24 final size:24
Alignment explanation
Indices: 240246--240358 Score: 106
Period size: 24 Copynumber: 4.7 Consensus size: 24
240236 ACCTTTGGAT
* *
240246 ACTCCTGTATTAGTGCAATTATGC
1 ACTCCTATATTAGTGCAATTGTGC
* * *
240270 ACTCTTCTACTAGTGC-ATTCGTGC
1 ACTCCTATATTAGTGCAATT-GTGC
240294 ACTCCTATAATTAGTGCAATTGTGC
1 ACTCCTAT-ATTAGTGCAATTGTGC
* *
240319 ACTCC-AGTATTAGTACCAA-TGTGT
1 ACTCCTA-TATTAGT-GCAATTGTGC
240343 ACTCCTATATTAGTGC
1 ACTCCTATATTAGTGC
240359 CACTTTGCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
23 4 0.05
24 45 0.62
25 21 0.29
26 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (24 bp):
ACTCCTATATTAGTGCAATTGTGC
Found at i:240311 original size:25 final size:24
Alignment explanation
Indices: 240246--240464 Score: 93
Period size: 24 Copynumber: 9.0 Consensus size: 24
240236 ACCTTTGGAT
* *
240246 ACTCCTGTATTAGTGCAATT-ATGC
1 ACTCCTATATTAGTGC-ATTCGTGC
* * *
240270 ACTCTTCTACTAGTGCATTCGTGC
1 ACTCCTATATTAGTGCATTCGTGC
240294 ACTCCTATAATTAGTGCAATT-GTGC
1 ACTCCTAT-ATTAGTGC-ATTCGTGC
* * *
240319 ACTCC-AGTATTAGTACCAAT-GTGT
1 ACTCCTA-TATTAGT-GCATTCGTGC
240343 ACTCCTATATTAGTGCCACTT--TGC
1 ACTCCTATATTAGTG-CA-TTCGTGC
* * *
240367 AATCTTGA-ATTAATGCATTCGTGC
1 ACTCCT-ATATTAGTGCATTCGTGC
* *
240391 ACT-CT-TGATTCGAGTACATTCGTGT
1 ACTCCTAT-ATT--AGTGCATTCGTGC
*
240416 AC-CC-ATTATTAGTGCATTTGTTGC
1 ACTCCTA-TATTAGTGCATTCG-TGC
*
240440 ACTTC-AGTATTAGTGCATTCGTGC
1 ACTCCTA-TATTAGTGCATTCGTGC
240464 A
1 A
240465 TTCATGTGTT
Statistics
Matches: 148, Mismatches: 27, Indels: 40
0.69 0.13 0.19
Matches are distributed among these distances:
22 2 0.01
23 17 0.11
24 73 0.49
25 52 0.35
26 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (24 bp):
ACTCCTATATTAGTGCATTCGTGC
Found at i:242352 original size:2 final size:2
Alignment explanation
Indices: 242345--242386 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
242335 TACGCAGTGA
242345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
242387 CAAATAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:243266 original size:25 final size:24
Alignment explanation
Indices: 243225--243274 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
243215 TAGGTCCTCA
*
243225 TATTTTAGGTTTATTTTATTTTATT
1 TATTTTAGGTTTATTTT-GTTTATT
*
243250 TATTTTATGTTGT-TTTTGTTTATT
1 TATTTTAGGTT-TATTTTGTTTATT
243274 T
1 T
243275 GTTTATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 7 0.32
25 14 0.64
26 1 0.05
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (24 bp):
TATTTTAGGTTTATTTTGTTTATT
Found at i:244277 original size:39 final size:39
Alignment explanation
Indices: 244227--244309 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 39
244217 TTGAACTCAA
244227 AATTTCCGATTTTAAATATAGGGTAATCAACTAGGTACC
1 AATTTCCGATTTTAAATATAGGGTAATCAACTAGGTACC
*
244266 AATTTCTGATTTTAAATATAGGGTAATCAACTAGGTACC
1 AATTTCCGATTTTAAATATAGGGTAATCAACTAGGTACC
244305 AATTT
1 AATTT
244310 TTGGGCGCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (39 bp):
AATTTCCGATTTTAAATATAGGGTAATCAACTAGGTACC
Found at i:248453 original size:20 final size:20
Alignment explanation
Indices: 248416--248454 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
248406 TCTAAATCAT
*
248416 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATATCATTTTGA
248436 TTTTCAAAATCATC-TTTTG
1 TTTTCAAAAT-ATCATTTTG
248455 CTTTCAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGA
Found at i:251339 original size:19 final size:20
Alignment explanation
Indices: 251317--251355 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
251307 AGTTGTGGCC
251317 ATTTCTAGCCG-TTGGGGAT
1 ATTTCTAGCCGTTTGGGGAT
*
251336 ATTTCTAGTCGTTTGGGGAT
1 ATTTCTAGCCGTTTGGGGAT
251356 GAAATCTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.41
Consensus pattern (20 bp):
ATTTCTAGCCGTTTGGGGAT
Found at i:252488 original size:21 final size:20
Alignment explanation
Indices: 252448--252489 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
252438 AGTTGTGGCC
*
252448 ATTTCTAACCGTTGGGGATG
1 ATTTCTAACCGTTAGGGATG
*
252468 ATTTCTAGCCGTTTAGGGATG
1 ATTTCTAACCG-TTAGGGATG
252489 A
1 A
252490 AATGTCTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (20 bp):
ATTTCTAACCGTTAGGGATG
Found at i:253719 original size:20 final size:20
Alignment explanation
Indices: 253691--253730 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
253681 TTAAAAAAAG
253691 TTAAATCTTTCATATTTATA
1 TTAAATCTTTCATATTTATA
* * *
253711 TTAACTCTTTTATTTTTATA
1 TTAAATCTTTCATATTTATA
253731 ATATTATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAAATCTTTCATATTTATA
Found at i:254488 original size:31 final size:31
Alignment explanation
Indices: 254452--254522 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
254442 CGATGGATGT
254452 CAATTCAACTTCTAGAAGCAATCAATGGATA
1 CAATTCAACTTCTAGAAGCAATCAATGGATA
254483 CAATTCAACTTCTAGAAGCAATCAATGGATA
1 CAATTCAACTTCTAGAAGCAATCAATGGATA
*
254514 CAACTCAAC
1 CAATTCAAC
254523 GAATGCTCGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24
Consensus pattern (31 bp):
CAATTCAACTTCTAGAAGCAATCAATGGATA
Found at i:256121 original size:22 final size:22
Alignment explanation
Indices: 256091--256136 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
256081 TTGATTTTAA
256091 TATTATTATATTATAATTA-TAT
1 TATTATTATATTAT-ATTACTAT
* *
256113 TATTCTTATGTTATATTACTAT
1 TATTATTATATTATATTACTAT
256135 TA
1 TA
256137 ATAGTTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTATTATATTATATTACTAT
Found at i:256190 original size:15 final size:15
Alignment explanation
Indices: 256170--256199 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
256160 AATGTAAAGC
256170 CCGAATTACAACCTG
1 CCGAATTACAACCTG
256185 CCGAATTACAACCTG
1 CCGAATTACAACCTG
256200 AAGGTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (15 bp):
CCGAATTACAACCTG
Found at i:259864 original size:3 final size:3
Alignment explanation
Indices: 259856--259912 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
259846 TAAAATTATT
*
259856 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TATT TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA
259900 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
259913 TTTAATAGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 6 0.13
3 36 0.77
4 5 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:259884 original size:22 final size:24
Alignment explanation
Indices: 259856--259910 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 24
259846 TAAAATTATT
259856 TAATAATAATATAATATAT-ATAA
1 TAATAATAATATAATATATAATAA
*
259879 T-ATAAT-A-ATAATATTTAATAA
1 TAATAATAATATAATATATAATAA
259900 TAATAATAATA
1 TAATAATAATA
259911 ATTTTAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 8 0.30
21 6 0.22
22 10 0.37
23 2 0.07
24 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TAATAATAATATAATATATAATAA
Found at i:259889 original size:25 final size:22
Alignment explanation
Indices: 259856--259924 Score: 92
Period size: 21 Copynumber: 3.3 Consensus size: 22
259846 TAAAATTATT
*
259856 TAATAATAAT-ATAATATAT-A
1 TAATAATAATAATAATATTTAA
259876 TAAT-ATAATAATAATATTTAA
1 TAATAATAATAATAATATTTAA
259897 TAATAATAATAATAAT-TTTAA
1 TAATAATAATAATAATATTTAA
*
259918 TAGTAAT
1 TAATAAT
259925 TTAAGTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
19 5 0.11
20 12 0.27
21 16 0.36
22 11 0.25
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (22 bp):
TAATAATAATAATAATATTTAA
Found at i:260179 original size:75 final size:75
Alignment explanation
Indices: 260099--260535 Score: 829
Period size: 75 Copynumber: 5.8 Consensus size: 75
260089 CGAGGGTTTA
*
260099 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
1 AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
*
260164 CGAAGGCTTT
66 CTAAGGCTTT
*
260174 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
1 AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
260239 CTAAGGCTTT
66 CTAAGGCTTT
*
260249 AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGAACTGAAGGACTTACAGATGACC
1 AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
260314 CTAAGGCTTT
66 CTAAGGCTTT
*
260324 AAAACATCAAAAAGATCCCGAAAGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
1 AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
260389 CTAAGGCTTT
66 CTAAGGCTTT
260399 AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
1 AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
260464 CTAAGGCTTT
66 CTAAGGCTTT
260474 AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
260536 TGGGAAATAG
Statistics
Matches: 356, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 356 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (75 bp):
AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
CTAAGGCTTT
Found at i:261070 original size:112 final size:113
Alignment explanation
Indices: 260939--261949 Score: 1439
Period size: 112 Copynumber: 9.0 Consensus size: 113
260929 ATAGAATTAT
* *
260939 GCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
261004 ATTATGAAC-TTCTCTGGCAAAGCTGCTCCATCAAGTGATGGATTTTA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
261051 GCAAAAGGTTGAACAAATTCTTCTTATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
261116 ATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
261164 GC-AAAGGTTGAACAAATTTTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
261228 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
261276 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
261341 ATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * *
261389 GC-AAAGGTTGAACAAATTTTTCTTATTATGAACTTCTTCTTCCTTCCTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
261453 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
** * *
261501 GC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * * *
261565 ATTATGAAC-TTCTCTGGAAAAAATAATTCATCAAGTGAT-GAATTCA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
261611 GGGAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
** * ** ** * *
261676 CATTATGAACTTTAACTGGCACTGCTGATCCA-CTGGGTGATGAATTTAA
65 CATTATGAACTTTCTCTGGAAAAGCTGATCCATC-AAGTGATGGATTTGA
* * *
261725 GCAAAAAGTTGACCAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * *
261790 ATTATGAACTTCCTCTGGAAAAGATAATCCATCAATTGAT-GAATTCA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * * *
261837 GGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTT-TTTAGATAAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
261901 CATTATGAACTTTCTCTGGAAATG-TCAATCCATCAAATGATAGATTTGA
65 CATTATGAACTTTCTCTGGAAAAGCT-GATCCATCAAGTGATGGATTTGA
261950 ATCTTTGCTA
Statistics
Matches: 806, Mismatches: 82, Indels: 21
0.89 0.09 0.02
Matches are distributed among these distances:
110 5 0.01
111 28 0.03
112 474 0.59
113 294 0.36
114 5 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:261336 original size:225 final size:225
Alignment explanation
Indices: 260941--261949 Score: 1467
Period size: 225 Copynumber: 4.5 Consensus size: 225
260931 AGAATTATGC
*
260941 AAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
261006 TATGAAC-TTCTCTGGCAAAGCTGCTCCATCAAGTGATGGATTTTAGCAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
* *
261070 CTTCTTATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
261135 AAAACTGATCCATCAAGTGATGGATTTGAG
196 AAAACTAATCCATCAAGTGATGGATTTGAG
* *
261165 CAAAGGTTGAACAAATTTTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
261230 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
*
261295 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
261360 AAAACTGATCCATCAAGTGATGGATTTGAG
196 AAAACTAATCCATCAAGTGATGGATTTGAG
* * *
261390 CAAAGGTTGAACAAATTTTTCTTATTATGAACTTCTTCTTCCTTCCTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**
261455 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC-AAAGGTTGAACAAGCT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
* *
261519 CTTCTCATTATGAACTTTTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAAC-TTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
* * * * *
261583 AAAAATAATTCATCAAGTGATGAATTCAGGG
196 AAAACTAATCCATCAAGTGATGGATT-TGAG
* *
261614 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * ** ** * * * * *
261679 TATGAACTTTAACTGGCACTGCTGATCCA-CTGGGTGATGAATTTAAGCAAAAAGTTGACCAAGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATC-AAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
*
261743 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * *
261808 AAAAGA-TAATCCATCAATTGAT-GAATTCAGG
195 AAAA-ACTAATCCATCAAGTGATGGATTTGA-G
* * * *
261839 TAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTT-TTTAGATAAGTTCTTCTCA
1 -AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
261903 TTATGAACTTTCTCTGGAAATG-TCAATCCATCAAATGATAGATTTGA
65 TTATGAACTTTCTCTGGAAAAGCT-GATCCATCAAGTGATGGATTTGA
261950 ATCTTTGCTA
Statistics
Matches: 714, Mismatches: 61, Indels: 19
0.90 0.08 0.02
Matches are distributed among these distances:
223 32 0.04
224 235 0.33
225 376 0.53
226 70 0.10
227 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (225 bp):
AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAACTAATCCATCAAGTGATGGATTTGAG
Found at i:261784 original size:449 final size:451
Alignment explanation
Indices: 260941--261949 Score: 1469
Period size: 449 Copynumber: 2.2 Consensus size: 451
260931 AGAATTATGC
*
260941 AAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
261006 TATGAAC-TTCTCTGGCAAAGCTGCTCCATCAAGTGATGGATTTTAGCAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAACT
*
261070 CTTCTTATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
* * * * * * *
261135 AAAACTGATCCATCAAGTGATGGATTTGAGCAAAGGTTGAACAAATTTTTCTTATTATGAACTTC
196 AAAAATAATCCATCAAGTGATGAATTAGAGAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
**
261200 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGT
261 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTGGAAAAGCTGATCCATCAAGT
* * * *
261265 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
326 GATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
* * * *
261330 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAA-ACTGATCCATCAAGTGATGGATT-TGAG-
391 GAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGA-TAATCCATCAAGTGATGAATTCAG-GT
* * *
261390 CAAAGGTTGAACAAATTTTTCTTATTATGAACTTCTTCTTCCTTCCTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
261455 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC-AAAGGTTGAACAAGCT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAACT
* * *
261519 CTTCTCATTATGAACTTTTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAAC-TTCTCTGGA
131 CTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
* * *
261583 AAAAATAATTCATCAAGTGATGAATTCAGGGAAAAGGTTGAACAAATTCTTCTCATTATGAATTT
196 AAAAATAATCCATCAAGTGATGAATT-AGAGAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
* ** **
261648 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTGGCACTGCTGATCCA-CTGG
260 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTGGAAAAGCTGATCCATC-AA
* *
261712 GTGATGAATTTAAGCAAAAAGTTGACCAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
324 GTGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
261777 ATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
389 ATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGT
* * * *
261840 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTT-TTTAGATAAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
261904 TATGAACTTTCTCTGGAAATG-TCAATCCATCAAATGATAGATTTGA
66 TATGAACTTTCTCTGGAAAAGCT-GATCCATCAAGTGATGGATTTGA
261950 ATCTTTGCTA
Statistics
Matches: 501, Mismatches: 52, Indels: 14
0.88 0.09 0.02
Matches are distributed among these distances:
448 33 0.07
449 389 0.78
450 79 0.16
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (451 bp):
AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAACT
CTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAAATAATCCATCAAGTGATGAATTAGAGAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTGGAAAAGCTGATCCATCAAGT
GATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
GAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGT
Found at i:262375 original size:22 final size:22
Alignment explanation
Indices: 262350--262404 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
262340 GATAAAGCTT
*
262350 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
262372 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
262394 TCATCTTTGAA
1 TCATCTTTGAA
262405 GAGTATAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:263534 original size:35 final size:34
Alignment explanation
Indices: 263495--263567 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 34
263485 CATTACTTCT
263495 TATTGAGATGAGCCTTCAAAATGCCCAAATATTC
1 TATTGAGATGAGCCTTCAAAATGCCCAAATATTC
** *
263529 ATATTGTTATGAGCCTTCAAAATGCCCCAATATTC
1 -TATTGAGATGAGCCTTCAAAATGCCCAAATATTC
263564 TATT
1 TATT
263568 TCTGGTGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 4 0.11
35 31 0.89
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (34 bp):
TATTGAGATGAGCCTTCAAAATGCCCAAATATTC
Found at i:264819 original size:114 final size:114
Alignment explanation
Indices: 264524--264841 Score: 496
Period size: 115 Copynumber: 2.8 Consensus size: 114
264514 GATCATGCAG
* * * * * *
264524 TTCATCTTTCAATTCCAATGATCGGTTCTGGGATTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGG-TTCATACCAAATCAGATCAGATAACTCAAAGA
* * *
264589 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAAA
65 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAAA
*
264639 TTCATCTTTCAAATCTAATGATTGATTTTGGCGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGG-GTTCATACCAAATCAGATCAGATAACTCAAAGA
264704 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGC-AAA
65 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAAA
264753 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGG-GTTCATACCAAATCAGATCAGATAACTCAAAGA
*
264818 ACACTTCCAAAAGATGCTA-TGAGC
65 ACACTTCCAGAAGATGCTATTGAGC
264842 ACATTTATCT
Statistics
Matches: 189, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
113 5 0.03
114 84 0.44
115 99 0.52
116 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGGTTCATACCAAATCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAAA
Found at i:264905 original size:93 final size:92
Alignment explanation
Indices: 264744--264930 Score: 286
Period size: 93 Copynumber: 2.0 Consensus size: 92
264734 TATTTCTACC
* *
264744 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
1 ATGAGCAAATTCATCTTCCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATA
264809 ACTCAAAGAACACTTCCAAAAGATGCT
66 ACTCAAAGAACACTTCCAAAAGATGCT
* * * * *
264836 ATGAGCACATTTATCTTCCAAATTCAATGATTGGTTCTGTGG-TTTCATACCAAACCAGATCAGA
1 ATGAGCAAATTCATCTTCCAAATCCAATGATTGATT-T-TGGAGTTCATACCAAACCAGATCAGA
264900 TAACTCAAAGAACACTTCCAAAAGATGCT
64 TAACTCAAAGAACACTTCCAAAAGATGCT
264929 AT
1 AT
264931 TGGGTCTCCT
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
92 31 0.36
93 52 0.60
94 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (92 bp):
ATGAGCAAATTCATCTTCCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATA
ACTCAAAGAACACTTCCAAAAGATGCT
Found at i:267213 original size:12 final size:11
Alignment explanation
Indices: 267192--267221 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
267182 CTTGATTCAA
267192 TTTTTCTTTTT
1 TTTTTCTTTTT
267203 TTTTTCTTTTT
1 TTTTTCTTTTT
267214 TTTTTCTT
1 TTTTTCTT
267222 CTTTCTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:267226 original size:18 final size:17
Alignment explanation
Indices: 267192--267229 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
267182 CTTGATTCAA
267192 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTTTTTTTTC
267209 TTTTT-TTTTTCTTCTTTC
1 TTTTTCTTTTT-TT-TTTC
267227 TTT
1 TTT
267230 GCTGGATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 7 0.37
18 7 0.37
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTC
Found at i:270543 original size:14 final size:14
Alignment explanation
Indices: 270509--270562 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
270499 TTGTGCAATA
* *
270509 CAAATGCAAAGATG
1 CAAATGTAAATATG
270523 CCAAATGTAAATATG
1 -CAAATGTAAATATG
270538 CAAATGTAAA-ATTG
1 CAAATGTAAATA-TG
*
270552 TAAATGTAAAT
1 CAAATGTAAAT
270563 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.03
14 21 0.62
15 12 0.35
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:271956 original size:12 final size:12
Alignment explanation
Indices: 271939--271988 Score: 64
Period size: 12 Copynumber: 3.9 Consensus size: 12
271929 TATTGAATAA
271939 AATAAATAAAAT
1 AATAAATAAAAT
271951 AATAAATAATAAT
1 AATAAATAA-AAT
271964 ATATAAATAAAAAT
1 A-ATAAAT-AAAAT
*
271978 AATAAGTAAAA
1 AATAAATAAAA
271989 AAAATTGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
12 13 0.38
13 9 0.26
14 10 0.29
15 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
AATAAATAAAAT
Found at i:271956 original size:17 final size:16
Alignment explanation
Indices: 271938--271987 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
271928 TTATTGAATA
271938 AAATAAATAAAATAAT
1 AAATAAATAAAATAAT
*
271954 AAAT-AATAATAT-AT
1 AAATAAATAAAATAAT
271968 AAATAAA-AATAATAAGT
1 AAATAAATAA-AATAA-T
271985 AAA
1 AAA
271988 AAAAATTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 8 0.29
15 11 0.39
16 5 0.18
17 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AAATAAATAAAATAAT
Found at i:271990 original size:14 final size:13
Alignment explanation
Indices: 271939--271989 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
271929 TATTGAATAA
271939 AATAAAT-AAAAT
1 AATAAATAAAAAT
*
271951 AATAAATAATAAT
1 AATAAATAAAAAT
271964 ATATAAATAAAAAT
1 A-ATAAATAAAAAT
*
271978 AATAAGTAAAAA
1 AATAAATAAAAA
271990 AAATTGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
12 7 0.21
13 15 0.44
14 12 0.35
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (13 bp):
AATAAATAAAAAT
Found at i:271992 original size:17 final size:16
Alignment explanation
Indices: 271937--271992 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
271927 ATTATTGAAT
*
271937 AAAATAAATAA-AATA
1 AAAAAAAATAATAATA
* *
271952 ATAAATAATAATATATA
1 AAAAAAAATAATA-ATA
*
271969 AATAAAAATAATAAGTA
1 AAAAAAAATAATAA-TA
271986 AAAAAAA
1 AAAAAAA
271993 TTGAAAGAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 8 0.26
16 2 0.06
17 21 0.68
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAAAAAATAATAATA
Found at i:274167 original size:3 final size:3
Alignment explanation
Indices: 274159--274228 Score: 65
Period size: 3 Copynumber: 23.3 Consensus size: 3
274149 TAAAATTATT
*
274159 TAA TAA TAA -ATA TAA T-A TATA TAA T-A TAA TAA TAA TATT TAA TAA
1 TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA
**
274204 TAA TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
274229 TTAAGTAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
2 5 0.09
3 44 0.80
4 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:274186 original size:14 final size:12
Alignment explanation
Indices: 274159--274216 Score: 64
Period size: 13 Copynumber: 4.6 Consensus size: 12
274149 TAAAATTATT
274159 TAATAATAAATA
1 TAATAATAAATA
274171 TAATATATATAATA
1 TAATA-ATA-AATA
*
274185 TAATAATAATATT
1 TAATAATAA-ATA
274198 TAATAAT-AATAA
1 TAATAATAAAT-A
274210 TAATAAT
1 TAATAAT
274217 TTTAATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 2 0.05
12 14 0.35
13 15 0.38
14 9 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAATAATAAATA
Found at i:274227 original size:21 final size:22
Alignment explanation
Indices: 274155--274228 Score: 97
Period size: 21 Copynumber: 3.6 Consensus size: 22
274145 CCTGTAAAAT
274155 TATTTAATAAT-A-AAT-ATAA
1 TATTTAATAATAATAATAATAA
*
274174 TATAT-ATAAT-ATAATAATAA
1 TATTTAATAATAATAATAATAA
274194 TATTTAATAATAATAATAATAA
1 TATTTAATAATAATAATAATAA
274216 T-TTTAATAATAAT
1 TATTTAATAATAAT
274229 TTAAGTAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.12
19 7 0.14
20 8 0.16
21 17 0.35
22 11 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTTAATAATAATAATAATAA
Found at i:282359 original size:15 final size:15
Alignment explanation
Indices: 282339--282367 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
282329 TTTTGAGTTT
282339 CATTTTCTTGTGTTA
1 CATTTTCTTGTGTTA
282354 CATTTTCTTGTGTT
1 CATTTTCTTGTGTT
282368 CCAATCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.62
Consensus pattern (15 bp):
CATTTTCTTGTGTTA
Found at i:286401 original size:26 final size:26
Alignment explanation
Indices: 286370--286447 Score: 147
Period size: 26 Copynumber: 3.0 Consensus size: 26
286360 TAGTGTCTTA
286370 TAAAATATGACAAATTAAATTGTCAC
1 TAAAATATGACAAATTAAATTGTCAC
*
286396 TAAAATACGACAAATTAAATTGTCAC
1 TAAAATATGACAAATTAAATTGTCAC
286422 TAAAATATGACAAATTAAATTGTCAC
1 TAAAATATGACAAATTAAATTGTCAC
286448 GAACAAAACT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (26 bp):
TAAAATATGACAAATTAAATTGTCAC
Found at i:287470 original size:22 final size:22
Alignment explanation
Indices: 287440--287485 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
287430 TTGATTTTGA
287440 TATTATTATATTATAATTA-TAT
1 TATTATTATATTAT-ATTACTAT
* *
287462 TATTCTTATGTTATATTACTAT
1 TATTATTATATTATATTACTAT
287484 TA
1 TA
287486 ATAGTTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTATTATATTATATTACTAT
Found at i:287943 original size:19 final size:19
Alignment explanation
Indices: 287919--287964 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
287909 ATTGCATAAC
287919 TCACCACCCCTAGGGTGAG
1 TCACCACCCCTAGGGTGAG
287938 TCACCACCCCTAGGGTGAG
1 TCACCACCCCTAGGGTGAG
287957 TCACCACC
1 TCACCACC
287965 GTAGCTCCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.41, G:0.22, T:0.15
Consensus pattern (19 bp):
TCACCACCCCTAGGGTGAG
Found at i:288653 original size:29 final size:29
Alignment explanation
Indices: 288616--288673 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
288606 AAGAATAATT
*
288616 ATAATATTAGAATAT-TTTTATATATTAAG
1 ATAACATTAGAATATATTTTA-ATATTAAG
*
288645 ATAACATTATAATATAGTTTTAATATTAA
1 ATAACATTAGAATATA-TTTTAATATTAA
288674 ATATTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 7 0.28
31 5 0.20
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (29 bp):
ATAACATTAGAATATATTTTAATATTAAG
Found at i:289232 original size:8 final size:8
Alignment explanation
Indices: 289219--289287 Score: 81
Period size: 8 Copynumber: 8.5 Consensus size: 8
289209 TAAGATAAAG
289219 ATAAAATA
1 ATAAAATA
289227 AT-AAA-A
1 ATAAAATA
289233 ATAAAATA
1 ATAAAATA
289241 ATAAAATA
1 ATAAAATA
289249 ATAAAGATAA
1 ATAAA-AT-A
289259 GGATAAAATA
1 --ATAAAATA
289269 ATAAAATA
1 ATAAAATA
289277 AT-AAATA
1 ATAAAATA
289284 ATAA
1 ATAA
289288 TTATAAGATA
Statistics
Matches: 54, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
6 3 0.06
7 13 0.24
8 27 0.50
9 2 0.04
10 2 0.04
11 2 0.04
12 5 0.09
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (8 bp):
ATAAAATA
Found at i:289243 original size:3 final size:3
Alignment explanation
Indices: 289219--289293 Score: 54
Period size: 3 Copynumber: 26.3 Consensus size: 3
289209 TAAGATAAAG
* **
289219 ATA A-A ATA ATA AAA ATA A-A ATA ATA A-A ATA ATA A-A GATA AGG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
*
289261 ATA A-A ATA ATA A-A ATA ATAA ATA ATA ATT ATA A
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA A
289294 GATAATGATA
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
2 11 0.20
3 41 0.73
4 4 0.07
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:289244 original size:28 final size:27
Alignment explanation
Indices: 289213--289287 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 27
289203 AGAATTTAAG
289213 ATAAAGATAAAATAATAAAAATAAAATA
1 ATAAA-ATAAAATAATAAAAATAAAATA
**
289241 ATAAAATAATAA-AGATAAGGATAAAATA
1 ATAAAATAA-AATA-ATAAAAATAAAATA
289269 ATAAAATAATAAATAATAA
1 ATAAAAT-A-AAATAATAA
289288 TTATAAGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 5 0.12
28 26 0.65
29 7 0.17
30 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (27 bp):
ATAAAATAAAATAATAAAAATAAAATA
Found at i:289247 original size:22 final size:22
Alignment explanation
Indices: 289219--289287 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
289209 TAAGATAAAG
289219 ATAAAATAATAAAAATAAAATA
1 ATAAAATAATAAAAATAAAATA
* **
289241 ATAAAATAATAAAGAT--AAGG
1 ATAAAATAATAAAAATAAAATA
289261 ATAAAATAAT-AAAATAATAAATA
1 ATAAAATAATAAAAAT-A-AAATA
289284 ATAA
1 ATAA
289288 TTATAAGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.11
20 12 0.32
22 15 0.41
23 6 0.16
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (22 bp):
ATAAAATAATAAAAATAAAATA
Found at i:294050 original size:23 final size:22
Alignment explanation
Indices: 294024--294104 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
294014 ACACAACTGA
*
294024 GTGCATCCATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
294046 CGTGCATCGGTGCATC-TTC-ATG
1 -GTGCATCGATGCA-CATTCAAGG
* *
294068 GTGAATCAATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
294090 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
294105 TAATTAGTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
20 1 0.02
21 13 0.29
22 5 0.11
23 25 0.56
24 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:297846 original size:22 final size:21
Alignment explanation
Indices: 297802--297843 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
297792 ATAAGACTAT
297802 TATCATTTTTCAATTTTGAAA
1 TATCATTTTTCAATTTTGAAA
297823 TATCATTTTT-ATATTTTGAAA
1 TATCATTTTTCA-ATTTTGAAA
297844 ATAAAGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TATCATTTTTCAATTTTGAAA
Found at i:309748 original size:3 final size:3
Alignment explanation
Indices: 309742--309789 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
309732 ATATTTTTAA
309742 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
309790 TTAAGGTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:315297 original size:23 final size:23
Alignment explanation
Indices: 315271--315315 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
315261 AGGTTAAGGT
315271 TTTGGTTCA-GGCCCAGGTTTGGG
1 TTTGGTT-ATGGCCCAGGTTTGGG
*
315294 TTTGGTTATGGCCCGGGTTTGG
1 TTTGGTTATGGCCCAGGTTTGG
315316 ACATTTTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.07, C:0.16, G:0.40, T:0.38
Consensus pattern (23 bp):
TTTGGTTATGGCCCAGGTTTGGG
Found at i:315351 original size:3 final size:3
Alignment explanation
Indices: 315345--315425 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
315335 ATATTTTTAA
315345 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
315393 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
315426 TTAAGGTAAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:319452 original size:3 final size:3
Alignment explanation
Indices: 319444--319522 Score: 149
Period size: 3 Copynumber: 26.3 Consensus size: 3
319434 GGGTTTAGGT
319444 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
319492 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
319523 GTAAGGTAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:320316 original size:21 final size:21
Alignment explanation
Indices: 320292--320333 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
320282 GTCTTCGAAA
320292 AAAAATGAACGAATCTTAAAG
1 AAAAATGAACGAATCTTAAAG
320313 AAAAATGAACGAATCTTAAAG
1 AAAAATGAACGAATCTTAAAG
320334 TGATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (21 bp):
AAAAATGAACGAATCTTAAAG
Found at i:320948 original size:6 final size:5
Alignment explanation
Indices: 320925--321002 Score: 52
Period size: 6 Copynumber: 14.6 Consensus size: 5
320915 GTTATAAATG
*
320925 TTATA TTAAAA TTATA TTACTA TTATTA TTATA TTATTA TTATA --ACTA
1 TTATA TT-ATA TTATA TTA-TA TTA-TA TTATA TTA-TA TTATA TTA-TA
* *
320973 TTATA TTATA ATACA TTATTA TTATTA TTA
1 TTATA TTATA TTATA TTA-TA TTA-TA TTA
321003 CTTATTATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
3 1 0.02
4 2 0.03
5 26 0.44
6 30 0.51
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (5 bp):
TTATA
Found at i:320953 original size:3 final size:3
Alignment explanation
Indices: 320935--321015 Score: 78
Period size: 3 Copynumber: 27.3 Consensus size: 3
320925 TTATATTAAA
* * *
320935 ATT A-T ATT ACT ATT ATT ATT A-T ATT ATT ATT ATA ACT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
320980 ATA ATAC ATT ATT ATT ATT ATT ACTT ATT ATT ATT A
1 ATT AT-T ATT ATT ATT ATT ATT A-TT ATT ATT ATT A
321016 CATATTTTGC
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
2 6 0.09
3 53 0.83
4 5 0.08
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:320955 original size:17 final size:18
Alignment explanation
Indices: 320939--321015 Score: 81
Period size: 17 Copynumber: 4.4 Consensus size: 18
320929 ATTAAAATTA
* *
320939 TATTACTATTATTATTA-
1 TATTATTATTATTACTAT
*
320956 TATTATTATTATAACTAT
1 TATTATTATTATTACTAT
*
320974 TA-TATTA-TAATAC-AT
1 TATTATTATTATTACTAT
320989 TATTATTATTATTACTTAT
1 TATTATTATTATTAC-TAT
321008 TATTATTA
1 TATTATTA
321016 CATATTTTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
15 4 0.08
16 9 0.18
17 24 0.49
18 2 0.04
19 10 0.20
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATTATTATTACTAT
Found at i:331409 original size:8 final size:9
Alignment explanation
Indices: 331392--331464 Score: 105
Period size: 9 Copynumber: 8.1 Consensus size: 9
331382 TTCTTTGAAG
331392 ATGAAAAAA
1 ATGAAAAAA
331401 ATGAAAAAA
1 ATGAAAAAA
331410 ATG-AAAAA
1 ATGAAAAAA
331418 ATGAAAAAA
1 ATGAAAAAA
331427 ATG-AAAAA
1 ATGAAAAAA
331435 ATGAAAAAAA
1 ATG-AAAAAA
331445 ATGAAAAAA
1 ATGAAAAAA
*
331454 CAGGAAAAAA
1 -ATGAAAAAA
331464 A
1 A
331465 GAAGGAGGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
8 16 0.27
9 27 0.46
10 16 0.27
ACGTcount: A:0.77, C:0.01, G:0.12, T:0.10
Consensus pattern (9 bp):
ATGAAAAAA
Found at i:331462 original size:17 final size:17
Alignment explanation
Indices: 331396--331453 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
331386 TTGAAGATGA
331396 AAAAAATGAAAAAAATG
1 AAAAAATGAAAAAAATG
331413 AAAAAATGAAAAAAATG
1 AAAAAATGAAAAAAATG
331430 AAAAAATGAAAAAAAATG
1 AAAAAATG-AAAAAAATG
331448 AAAAAA
1 AAAAAA
331454 CAGGAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
17 25 0.62
18 15 0.38
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAAATGAAAAAAATG
Found at i:332811 original size:55 final size:55
Alignment explanation
Indices: 332743--333279 Score: 810
Period size: 55 Copynumber: 9.8 Consensus size: 55
332733 GTGAAGCAAA
* * **
332743 TGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGAGCAAACACGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
* * *
332798 TGAAGATTATTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
*
332853 TGAAGATTGCTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
* *
332908 TGAAGATTGTTTGAGTCTCATACTCTATGAAGAAATAGGGAGCAGGCACGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
*
332963 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCGGGCACGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
* * *
333018 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAACAGGGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
* *
333073 TGAAGATTGCTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCATGCACGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
* *
333128 TGAAGATTGTTCGAGTCTCACACTCTCTGAAGAAATAGGGAGCAGGCATGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
* * * * * *
333183 TGAAGGTTGTTCGAGTCTTATACTCTTTGAAAAAATAGGGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
*
333238 TGAAG-TTGTTCGAGATC-CATACT-TCCTGAAGCAATAGGGAGC
1 TGAAGATTGTTCGAG-TCTCATACTCT-CTGAAGAAATAGGGAGC
333280 GAACCCGCTG
Statistics
Matches: 440, Mismatches: 40, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
53 1 0.00
54 28 0.06
55 411 0.93
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
Found at i:333477 original size:11 final size:12
Alignment explanation
Indices: 333456--333522 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 12
333446 GTCCGGGTTA
333456 TAAATATTATAT
1 TAAATATTATAT
333468 TAAA-ATTATAT
1 TAAATATTATAT
*
333479 T-ACTATTATTAT
1 TAAATATTA-TAT
333491 T--ATATTATTAT
1 TAAATATTA-TAT
333502 TATAACTATTATAT
1 TA-AA-TATTATAT
333516 TATAATA
1 TA-AATA
333523 CATTATTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
10 1 0.02
11 22 0.47
12 8 0.17
13 2 0.04
14 9 0.19
15 5 0.11
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATATTATAT
Found at i:333485 original size:6 final size:5
Alignment explanation
Indices: 333459--333539 Score: 58
Period size: 6 Copynumber: 15.2 Consensus size: 5
333449 CGGGTTATAA
*
333459 ATATT ATATT AAAATT ATATT ACTATT ATTATT ATATT ATTATT ATA--
1 ATATT ATATT -ATATT ATATT A-TATT A-TATT ATATT A-TATT ATATT
* *
333506 ACTATT ATATT ATAAT ACATT ATTATT ATTATT A
1 A-TATT ATATT ATATT ATATT A-TATT A-TATT A
333540 CTTATTATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
3 1 0.02
4 2 0.03
5 29 0.47
6 30 0.48
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (5 bp):
ATATT
Found at i:333490 original size:3 final size:3
Alignment explanation
Indices: 333472--333552 Score: 78
Period size: 3 Copynumber: 27.3 Consensus size: 3
333462 TTATATTAAA
* * *
333472 ATT A-T ATT ACT ATT ATT ATT A-T ATT ATT ATT ATA ACT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
333517 ATA ATAC ATT ATT ATT ATT ATT ACTT ATT ATT ATT A
1 ATT AT-T ATT ATT ATT ATT ATT A-TT ATT ATT ATT A
333553 CATATTTTGC
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
2 6 0.09
3 53 0.83
4 5 0.08
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:333492 original size:17 final size:18
Alignment explanation
Indices: 333476--333552 Score: 81
Period size: 17 Copynumber: 4.4 Consensus size: 18
333466 ATTAAAATTA
* *
333476 TATTACTATTATTATTA-
1 TATTATTATTATTACTAT
*
333493 TATTATTATTATAACTAT
1 TATTATTATTATTACTAT
*
333511 TA-TATTA-TAATAC-AT
1 TATTATTATTATTACTAT
333526 TATTATTATTATTACTTAT
1 TATTATTATTATTAC-TAT
333545 TATTATTA
1 TATTATTA
333553 CATATTTTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
15 4 0.08
16 9 0.18
17 24 0.49
18 2 0.04
19 10 0.20
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATTATTATTACTAT
Found at i:333518 original size:20 final size:17
Alignment explanation
Indices: 333459--333550 Score: 78
Period size: 17 Copynumber: 5.1 Consensus size: 17
333449 CGGGTTATAA
**
333459 ATATTA-TATTAAAATT
1 ATATTATTATTATTATT
*
333475 ATATTACTATTATTATT
1 ATATTATTATTATTATT
333492 ATATTATTATTATAACTATT
1 ATATTATTATTAT---TATT
* *
333512 ATATTATAATACATTATT
1 ATATTATTAT-TATTATT
333530 ATTATTATTACTTATTATT
1 A-TATTATTA-TTATTATT
333549 AT
1 AT
333551 TACATATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
16 6 0.10
17 20 0.32
18 6 0.10
19 14 0.23
20 14 0.23
21 2 0.03
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTATTATTATTATT
Done.