Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008558.1 Hibiscus syriacus cultivar Beakdansim tig00111463_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: 2950132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1239402 original size:23 final size:22
Alignment explanation
Indices: 1239372--1239440 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
1239362 ATCCATTTGT
1239372 TTTTTATTTATATTATTATTATA
1 TTTTTA-TTATATTATTATTATA
1239395 TTTTTATTATTATTATTATTATTA
1 TTTTTATTA-TATTATTATTA-TA
** *
1239419 TTTAAAATTATTTTATTATTAT
1 TTT-TTATTATATTATTATTAT
1239441 TATTAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.08
23 18 0.45
24 15 0.38
25 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATTATATTATTATTATA
Found at i:1240826 original size:4 final size:4
Alignment explanation
Indices: 1240817--1240857 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1240807 AAATATAGTA
* *
1240817 ATTT ATTT ATTT ATTT ATTT ATTA ATAT -TTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
1240858 GTTGTATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 2 0.06
4 30 0.94
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:1240865 original size:15 final size:15
Alignment explanation
Indices: 1240817--1240857 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1240807 AAATATAGTA
*
1240817 ATTTATTTATTTATTT
1 ATTTATTTATAT-TTT
*
1240833 ATTTATTAATATTTT
1 ATTTATTTATATTTT
1240848 ATTTATTTAT
1 ATTTATTTAT
1240858 GTTGTATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTATTTATATTTT
Found at i:1242737 original size:102 final size:101
Alignment explanation
Indices: 1242467--1242778 Score: 378
Period size: 102 Copynumber: 3.1 Consensus size: 101
1242457 CATTTGAGAG
* *
1242467 TTTCAATTGAAACAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTT-TGTCATGCT
1 TTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTATCTCA--CT
* * * * *
1242531 TGAGA-CAGTTTTCGTTTGAAACTCAAATTTTGGAATTC
64 TGAGATAATTTTTC-CTTGAAACACAAATTTTGAAATTC
* * *
1242569 TTTCACTTG-AACAAAATTGATCTCGCTTGAGATTGTTTTCCTAAAAACAAATTTAGTTTCGCTT
1 TTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTA-TCTCACTT
1242633 GAGATAATTTTTCCTTGAAACACAAATTTTGAAATTC
65 GAGATAATTTTTCCTTGAAACACAAATTTTGAAATTC
* * * * * *
1242670 TTTCACTTGAAACTAATTTGATATAATTTGATATTGTTTTCCTAAAAACAAATTTCATCTCACTT
1 TTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTT-ATCTCACTT
* * * *
1242735 GAGATAATTTTACCTTCAAACACATATTTTGAAATTG
65 GAGATAATTTTTCCTTGAAACACAAATTTTGAAATTC
1242772 TTTCACT
1 TTTCACT
1242779 CGGAAAATTT
Statistics
Matches: 183, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
101 81 0.44
102 98 0.54
103 4 0.02
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (101 bp):
TTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTATCTCACTTG
AGATAATTTTTCCTTGAAACACAAATTTTGAAATTC
Found at i:1243513 original size:104 final size:104
Alignment explanation
Indices: 1243333--1243602 Score: 326
Period size: 104 Copynumber: 2.6 Consensus size: 104
1243323 GATTGACCCG
* * * * * *
1243333 ACTTCCTCAATGAGAAGGAACAATGTCATATGGAAGAGGCCAGAACTCTTCAATATGGATGAACA
1 ACTTCCTCAATAAGAAGGAACAATGTCATCTGAAAGAGACCAGAACTCTTCAACATGGATGGACA
* *
1243398 TTGTCATCTTCAACACCAAATTATCTCCAGCTTAAGTCA
66 GTGTCATCTTCAACACCAAATTATCTCCAGCTTAACTCA
* ** * * * *
1243437 ACTTCCTCAACAAGAAGGAACAAAATCATCTGAAAGCGTCTAGAACTCTTCAACATGGATGGCCA
1 ACTTCCTCAATAAGAAGGAACAATGTCATCTGAAAGAGACCAGAACTCTTCAACATGGATGGACA
* * * * *
1243502 GTGTCATCTTCAACACTAAATTATCTCTATCTTGACTCG
66 GTGTCATCTTCAACACCAAATTATCTCCAGCTTAACTCA
* *
1243541 ACTTCCTCAATAAGAAGGAACAATGTCATCT-AAAAATGACCACAACTCTTCAACATGGATGG
1 ACTTCCTCAATAAGAAGGAACAATGTCATCTGAAAGA-GACCAGAACTCTTCAACATGGATGG
1243603 GAAGCACCGT
Statistics
Matches: 138, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
103 3 0.02
104 135 0.98
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (104 bp):
ACTTCCTCAATAAGAAGGAACAATGTCATCTGAAAGAGACCAGAACTCTTCAACATGGATGGACA
GTGTCATCTTCAACACCAAATTATCTCCAGCTTAACTCA
Found at i:1243616 original size:104 final size:103
Alignment explanation
Indices: 1243313--1243629 Score: 293
Period size: 104 Copynumber: 3.1 Consensus size: 103
1243303 GTTATCTTTA
* * * * * *
1243313 AAATTATCT--AGATTGACCCGACTTCCTCAATGAGAAGGAACAATGTCATATGGAAGAGGCCAG
1 AAATTATCTCCAGCTTGACTCGACTTCCTCAATAAGAAGGAACAATGTCATCT-GAAAAGACCAG
* *
1243376 AACTCTTCAATATGGAT--GAA-CATTGTCATCTTCAACACC
65 AACTCTTCAACATGGATGGGAAGCA---TCATCTTCAACACT
* * * * ** * * *
1243415 AAATTATCTCCAGCTTAAGTCAACTTCCTCAACAAGAAGGAACAAAATCATCTGAAAGCGTCTAG
1 AAATTATCTCCAGCTTGACTCGACTTCCTCAATAAGAAGGAACAATGTCATCTGAAA-AGACCAG
** **
1243480 AACTCTTCAACATGGATGGCCAGTGTCATCTTCAACACT
65 AACTCTTCAACATGGATGGGAAGCATCATCTTCAACACT
* * * *
1243519 AAATTATCTCTATCTTGACTCGACTTCCTCAATAAGAAGGAACAATGTCATCTAAAAATGACCAC
1 AAATTATCTCCAGCTTGACTCGACTTCCTCAATAAGAAGGAACAATGTCATCTGAAAA-GACCAG
* *
1243584 AACTCTTCAACATGGATGGGAAGCACCGTCTTCAACACT
65 AACTCTTCAACATGGATGGGAAGCATCATCTTCAACACT
*
1243623 ATATTAT
1 AAATTAT
1243630 ATCTGGATTG
Statistics
Matches: 168, Mismatches: 40, Indels: 12
0.76 0.18 0.05
Matches are distributed among these distances:
102 9 0.05
103 3 0.02
104 155 0.92
106 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (103 bp):
AAATTATCTCCAGCTTGACTCGACTTCCTCAATAAGAAGGAACAATGTCATCTGAAAAGACCAGA
ACTCTTCAACATGGATGGGAAGCATCATCTTCAACACT
Found at i:1243641 original size:104 final size:104
Alignment explanation
Indices: 1243402--1243664 Score: 256
Period size: 104 Copynumber: 2.5 Consensus size: 104
1243392 TGAACATTGT
* * * * * *
1243402 CATCTTCAACACCAAATTATCTCCAGCTTAAGTCAACTTCCTCAACAAGAAGGAACAAAATCATC
1 CATCTTCAACACTAAATTATATCTAGATTGACTCAACTTCCTCAACAAGAAGGAACAAAATCATC
* * * * * * ***
1243467 TGAAAGCGTCTAGAACTCTTCAACATGGATGGCCAGTGT
66 TAAAAACGACCACAACTCTTCAACATGGATGGCAAGCAC
* ** * * **
1243506 CATCTTCAACACTAAATTATCTCTATCTTGACTCGACTTCCTCAATAAGAAGGAACAATGTCATC
1 CATCTTCAACACTAAATTATATCTAGATTGACTCAACTTCCTCAACAAGAAGGAACAAAATCATC
* *
1243571 TAAAAATGACCACAACTCTTCAACATGGATGGGAAGCAC
66 TAAAAACGACCACAACTCTTCAACATGGATGGCAAGCAC
* * * * * *
1243610 CGTCTTCAACACTATATTATATCTGGATTGACTCAACTTCCCCAACGATAAGGAA
1 CATCTTCAACACTAAATTATATCTAGATTGACTCAACTTCCTCAACAAGAAGGAA
1243665 TAGTATCATC
Statistics
Matches: 128, Mismatches: 31, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
104 128 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.26
Consensus pattern (104 bp):
CATCTTCAACACTAAATTATATCTAGATTGACTCAACTTCCTCAACAAGAAGGAACAAAATCATC
TAAAAACGACCACAACTCTTCAACATGGATGGCAAGCAC
Found at i:1243868 original size:3 final size:3
Alignment explanation
Indices: 1243853--1243895 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
1243843 GTTTGGGTTT
1243853 TTA TTA TTCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1243896 ATAATACTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1254354 original size:47 final size:44
Alignment explanation
Indices: 1254141--1254413 Score: 266
Period size: 44 Copynumber: 6.1 Consensus size: 44
1254131 TCTATGACTT
** *
1254141 GTAAGACCTTACTGTTTCTGCAGGCTCCTCTGCT-TAGTGCAAGG
1 GTAAGACCTTACCATTTCTGCAAGCTCCTCTGCTAT-GTGCAAGG
* * * *
1254185 GTAAGACCTTACCGTTTCT--ATAGCCTCTTCTGCTAAGTACAAGG
1 GTAAGACCTTACCATTTCTGCA-AG-CTCCTCTGCTATGTGCAAGG
* * * *
1254229 GTACGACCTTACCATTTCTGCAAGCTCCTCTACTATCTGAAAGG
1 GTAAGACCTTACCATTTCTGCAAGCTCCTCTGCTATGTGCAAGG
* *
1254273 GTAAGACCTTACCGTTTCTGC-AGACTTCTCTGCTATGTGCAAGG
1 GTAAGACCTTACCATTTCTGCAAG-CTCCTCTGCTATGTGCAAGG
* * *
1254317 GTAAGACCTAATTATCATTTCTACAAGCTCCTCTGCTAAGTGCAAGG
1 GTAAGACC---TTACCATTTCTGCAAGCTCCTCTGCTATGTGCAAGG
* * * *
1254364 GTAAGACCTTACCATTTATGTAGGCTCCTCTGCTTTGTGCACAGG
1 GTAAGACCTTACCATTTCTGCAAGCTCCTCTGCTATGTGCA-AGG
1254409 GTAAG
1 GTAAG
1254414 CCCCTACTAG
Statistics
Matches: 187, Mismatches: 31, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
42 1 0.01
43 3 0.02
44 134 0.72
45 10 0.05
46 1 0.01
47 36 0.19
48 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (44 bp):
GTAAGACCTTACCATTTCTGCAAGCTCCTCTGCTATGTGCAAGG
Found at i:1254395 original size:91 final size:88
Alignment explanation
Indices: 1254141--1254413 Score: 312
Period size: 88 Copynumber: 3.1 Consensus size: 88
1254131 TCTATGACTT
** * * *
1254141 GTAAGACCTTACTGTTTCTGCAGGCTCCTCTGCTTAGTGCAAGGGTAAGACCTTACCGTTTCTAT
1 GTAAGACCTTACCATTTCTGCAAGCTCCTCTGCTAAGTGCAAGGGTAAGACCTTACCGTTTCTGT
* * * *
1254206 AGCCTCTTCTGCTAAGTACAAGG
66 AGACTCCTCTGCTATGTGCAAGG
* * ** * *
1254229 GTACGACCTTACCATTTCTGCAAGCTCCTCTACTATCTGAAAGGGTAAGACCTTACCGTTTCTGC
1 GTAAGACCTTACCATTTCTGCAAGCTCCTCTGCTAAGTGCAAGGGTAAGACCTTACCGTTTCTGT
*
1254294 AGACTTCTCTGCTATGTGCAAGG
66 AGACTCCTCTGCTATGTGCAAGG
* * * *
1254317 GTAAGACCTAATTATCATTTCTACAAGCTCCTCTGCTAAGTGCAAGGGTAAGACCTTACCATTTA
1 GTAAGACC---TTACCATTTCTGCAAGCTCCTCTGCTAAGTGCAAGGGTAAGACCTTACCGTTTC
* *
1254382 TGTAGGCTCCTCTGCTTTGTGCACAGG
63 TGTAGACTCCTCTGCTATGTGCA-AGG
1254409 GTAAG
1 GTAAG
1254414 CCCCTACTAG
Statistics
Matches: 152, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
88 79 0.52
91 65 0.43
92 8 0.05
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (88 bp):
GTAAGACCTTACCATTTCTGCAAGCTCCTCTGCTAAGTGCAAGGGTAAGACCTTACCGTTTCTGT
AGACTCCTCTGCTATGTGCAAGG
Found at i:1254799 original size:21 final size:23
Alignment explanation
Indices: 1254775--1254818 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1254765 GTATATATTT
*
1254775 TATACA-ATTTTTTTA-CATATG
1 TATACATATATTTTTATCATATG
1254796 TATACATATATTTTTATCATATG
1 TATACATATATTTTTATCATATG
1254819 AATCTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 8 0.40
23 6 0.30
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (23 bp):
TATACATATATTTTTATCATATG
Found at i:1261103 original size:44 final size:44
Alignment explanation
Indices: 1261040--1261350 Score: 451
Period size: 44 Copynumber: 7.1 Consensus size: 44
1261030 TTCAGGCCTG
* *
1261040 TACCGTTTCTGCAGGCTCCTCTGCTAAGTGTAAGGGTAAGACAT
1 TACCGTTTCTGCAGGCTCCTCTGCTAAGTGCAAGGGTAAGACCT
1261084 TACCGTTTCTGCAGGCTCCTCTGCTAAGTGCAAGGGTAAGACCT
1 TACCGTTTCTGCAGGCTCCTCTGCTAAGTGCAAGGGTAAGACCT
* * * *
1261128 TACCATTTTTGCAGGCTCCTTTGCTAAGTGCAAGGGTAAGAACT
1 TACCGTTTCTGCAGGCTCCTCTGCTAAGTGCAAGGGTAAGACCT
* * * * *
1261172 TATCATTTCTGCAGGCTCTTCTCCTATGTGCAAGGGTAAGACCT
1 TACCGTTTCTGCAGGCTCCTCTGCTAAGTGCAAGGGTAAGACCT
* *
1261216 TACCGTTTATGCAGGCTCCTATGCTAAGTGCAAGGGTAAGACCT
1 TACCGTTTCTGCAGGCTCCTCTGCTAAGTGCAAGGGTAAGACCT
* * *
1261260 TACCATTTCTGTAGGCTCCTCTGCTACGTGCAAGGGTAAGACCT
1 TACCGTTTCTGCAGGCTCCTCTGCTAAGTGCAAGGGTAAGACCT
* * *
1261304 TACCGTTTCTGCAGGCTCCTCTACTATGTACAAGGGTAAGACCT
1 TACCGTTTCTGCAGGCTCCTCTGCTAAGTGCAAGGGTAAGACCT
1261348 TAC
1 TAC
1261351 TACTTTCCGT
Statistics
Matches: 237, Mismatches: 30, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 237 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (44 bp):
TACCGTTTCTGCAGGCTCCTCTGCTAAGTGCAAGGGTAAGACCT
Found at i:1261415 original size:39 final size:39
Alignment explanation
Indices: 1261359--1261437 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 39
1261349 ACTACTTTCC
* *
1261359 GTAGGCTCCTTGGCTTTGTACTCAGGGTAAGTCC-TTACT
1 GTAGGCTCCTTGACTTTGTACACAGGGTAAG-CCGTTACT
*
1261398 GTAGGCTCCTCT-ACTTTGTGCACAGGGTAAGCCGTTACT
1 GTAGGCTCCT-TGACTTTGTACACAGGGTAAGCCGTTACT
1261437 G
1 G
1261438 GGTGTACAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 2 0.06
39 32 0.91
40 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (39 bp):
GTAGGCTCCTTGACTTTGTACACAGGGTAAGCCGTTACT
Found at i:1263973 original size:19 final size:20
Alignment explanation
Indices: 1263951--1263988 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1263941 GAACAAAAAC
*
1263951 ATAAAT-AACATAAATATAA
1 ATAAATAAACAAAAATATAA
1263970 ATAAATAAACAAAAATATA
1 ATAAATAAACAAAAATATA
1263989 TGGTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
ATAAATAAACAAAAATATAA
Found at i:1265423 original size:3 final size:3
Alignment explanation
Indices: 1265411--1265458 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
1265401 TAATTTGTAT
1265411 TAA TAA -AA 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
1265458 T
1 T
1265459 TTAAAAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1265626 original size:41 final size:42
Alignment explanation
Indices: 1265574--1265657 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 42
1265564 ATCATCCTTT
* *
1265574 AAAACTGGATTGGTAAATAAAATTTGAGATAATATCAT-TTA
1 AAAACTAGATTGATAAATAAAATTTGAGATAATATCATATTA
*
1265615 AAAACTAGATTGATAAATAAAATTTGGGATAATATCATATTA
1 AAAACTAGATTGATAAATAAAATTTGAGATAATATCATATTA
1265657 A
1 A
1265658 GACTCAGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 35 0.90
42 4 0.10
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (42 bp):
AAAACTAGATTGATAAATAAAATTTGAGATAATATCATATTA
Found at i:1267285 original size:37 final size:37
Alignment explanation
Indices: 1267244--1267317 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1267234 ATTAATACCT
1267244 CCGTATCCTAATGTTGAGAATCTTGTACAAAGAGGCC
1 CCGTATCCTAATGTTGAGAATCTTGTACAAAGAGGCC
1267281 CCGTATCCTAATGTTGAGAATCTTGTACAAAGAGGCC
1 CCGTATCCTAATGTTGAGAATCTTGTACAAAGAGGCC
1267318 TTCATCGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (37 bp):
CCGTATCCTAATGTTGAGAATCTTGTACAAAGAGGCC
Found at i:1268832 original size:84 final size:83
Alignment explanation
Indices: 1268644--1268833 Score: 226
Period size: 84 Copynumber: 2.3 Consensus size: 83
1268634 TTATTTTATC
* * * **
1268644 TTTAGGAATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGGATATTATTTTTATTA
1 TTTAGGAATTTAAGTATAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTAGGA
*
1268709 TATTTTATCTTATCTTTGT
66 TA-TTTATCTTAGCTTTGT
* *
1268728 TTTAGGAATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTA-TTTTAGGA
1 TTTAGGAATTTAAGTATAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTAGGA
1268792 -A-TTATCTTTAGC-TTGTT
66 TATTTATC-TTAGCTTTG-T
1268809 TTTAGGAATTTGAAGGCTATAAATA
1 TTTAGGAATTT-AA-G-TATAAATA
1268834 CCCTCTCAGG
Statistics
Matches: 95, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
80 8 0.08
81 16 0.17
82 2 0.02
83 7 0.07
84 62 0.65
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (83 bp):
TTTAGGAATTTAAGTATAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTAGGA
TATTTATCTTAGCTTTGT
Found at i:1269438 original size:19 final size:19
Alignment explanation
Indices: 1269410--1269456 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1269400 CTTTAAATTA
*
1269410 TTTA-TTTAATTATTTTCT
1 TTTATTTTAATTATTATCT
*
1269428 TTTATTTTAATTCTTATCT
1 TTTATTTTAATTATTATCT
1269447 TTTATTTTAA
1 TTTATTTTAA
1269457 AAACAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTTTAATTATTATCT
Found at i:1269560 original size:19 final size:20
Alignment explanation
Indices: 1269524--1269569 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1269514 TTTTCCCATT
*
1269524 TATTTATTATTATTATTATA
1 TATTTTTTATTATTATTATA
1269544 TATTTTTTATT-TTATTATA
1 TATTTTTTATTATTATTATA
*
1269563 TCTTTTT
1 TATTTTT
1269570 AACTTCATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTTTATTATTATTATA
Found at i:1269561 original size:22 final size:21
Alignment explanation
Indices: 1269478--1269561 Score: 89
Period size: 22 Copynumber: 3.7 Consensus size: 21
1269468 AAAAATCCCC
*
1269478 TTTTTATCTTTATTACTATTAT
1 TTTTTAT-TTTATTATTATTAT
1269500 TTTTTATTTTATTATT-TTCCCAT
1 TTTTTATTTTATTATTATT---AT
1269523 TTATTTATTATTATTATTATATAT
1 TT-TTTATT-TTATTATTAT-TAT
1269547 TTTTTATTTTATTAT
1 TTTTTATTTTATTAT
1269562 ATCTTTTTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
20 2 0.04
21 8 0.15
22 14 0.26
23 10 0.19
24 10 0.19
25 8 0.15
26 1 0.02
27 1 0.02
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTATTTTATTATTATTAT
Found at i:1271093 original size:59 final size:59
Alignment explanation
Indices: 1270968--1271299 Score: 505
Period size: 59 Copynumber: 5.7 Consensus size: 59
1270958 TCCCATACAT
* * * *
1270968 AAATTCATACACTTAGTATGAATTTCTTATCA-TTTAGCACATAAGGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCTATACGG
*
1271026 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCTATACGG
* *
1271085 AAAATCATACACTTAGTATGAATTTCTTAACATTTTAGCTCACAAAGTGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCTATACGG
** * *
1271144 AAATTCATACACTTAGTATGAATTTCTTAACATTTTATTACACAAAGTTCCCTATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCTATACGG
* *
1271203 AAATTCATACACTTAGTATGAATTTCTTAGCATTTTAGCACACGAAGTGCCCTAT----
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCTATACGG
1271258 -AATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
1271300 TTAGTGTCAT
Statistics
Matches: 253, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
54 41 0.16
58 31 0.12
59 181 0.72
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCTATACGG
Found at i:1271655 original size:20 final size:22
Alignment explanation
Indices: 1271630--1271681 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1271620 TAGTTCTTCA
*
1271630 GTATCGATACT-CCC-ACCATG
1 GTATCGATACTACCCTAACATG
*
1271650 GTATCGATACTACCCTAATATG
1 GTATCGATACTACCCTAACATG
1271672 GTATCGATAC
1 GTATCGATAC
1271682 CCCCTTCCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.39
21 3 0.11
22 14 0.50
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (22 bp):
GTATCGATACTACCCTAACATG
Found at i:1271749 original size:20 final size:21
Alignment explanation
Indices: 1271724--1271775 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
1271714 GATGTGGCCC
*
1271724 GGTATCGATAC-CTTTACCAT
1 GGTATCGATACACTATACCAT
*
1271744 GGTATCGATACTACTATACTAT
1 GGTATCGATAC-ACTATACCAT
1271766 GGTATCGATA
1 GGTATCGATA
1271776 TGCCCTTCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (21 bp):
GGTATCGATACACTATACCAT
Found at i:1271793 original size:95 final size:95
Alignment explanation
Indices: 1271644--1271829 Score: 264
Period size: 95 Copynumber: 2.0 Consensus size: 95
1271634 CGATACTCCC
* *
1271644 ACCATGGTATCGATACTACCCTAATATGGTATCGATACCCCCTTCCAGTATCGATACCAAAATTT
1 ACCATGGTATCGATACTACCATAATATGGTATCGATACCCCCTTCCAGTATCGATACCAAAATTA
*
1271709 GATTTGATGTGGCCCGGTATCGATACCTTT
66 GATTTGATGTGACCCGGTATCGATACCTTT
* * ** **
1271739 ACCATGGTATCGATACTACTATACTATGGTATCGATATGCCCTTCTGGTATCGATACCAAAATTA
1 ACCATGGTATCGATACTACCATAATATGGTATCGATACCCCCTTCCAGTATCGATACCAAAATTA
* * *
1271804 GGTTTGATGTTACCTGGTATCGATAC
66 GATTTGATGTGACCCGGTATCGATAC
1271830 TACCTCGTCG
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
95 79 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (95 bp):
ACCATGGTATCGATACTACCATAATATGGTATCGATACCCCCTTCCAGTATCGATACCAAAATTA
GATTTGATGTGACCCGGTATCGATACCTTT
Found at i:1277276 original size:17 final size:18
Alignment explanation
Indices: 1277254--1277287 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1277244 CAAGGAAACC
*
1277254 CATTTTGTTTT-ATTTTT
1 CATTTTATTTTCATTTTT
1277271 CATTTTATTTTCATTTT
1 CATTTTATTTTCATTTT
1277288 AATTTCGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (18 bp):
CATTTTATTTTCATTTTT
Found at i:1277281 original size:11 final size:11
Alignment explanation
Indices: 1277261--1277353 Score: 52
Period size: 11 Copynumber: 8.8 Consensus size: 11
1277251 ACCCATTTTG
1277261 TTTTATTTTTCA
1 TTTTA-TTTTCA
1277273 TTTTATTTTCA
1 TTTTATTTTCA
* *
1277284 TTTTAATTTCG
1 TTTTATTTTCA
* *
1277295 CTTTATTTTTA
1 TTTTATTTTCA
* ** *
1277306 GTAAAATTT-A
1 TTTTATTTTCA
* *
1277316 TTTCA-TTCCA
1 TTTTATTTTCA
1277326 -TTTATTTT-A
1 TTTTATTTTCA
1277335 TTTTATTTT-A
1 TTTTATTTTCA
1277345 TTTTATTTT
1 TTTTATTTT
1277354 ATCATATGCT
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
9 6 0.10
10 24 0.39
11 27 0.44
12 5 0.08
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:1277334 original size:5 final size:5
Alignment explanation
Indices: 1277326--1277380 Score: 65
Period size: 5 Copynumber: 10.6 Consensus size: 5
1277316 TTTCATTCCA
** *
1277326 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT CATAT GCTTAAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT --TTTAT TTTAT TTTAT
1277378 TTT
1 TTT
1277381 TCTCTGAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
5 40 0.95
7 2 0.05
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:1286531 original size:84 final size:84
Alignment explanation
Indices: 1286390--1286560 Score: 274
Period size: 84 Copynumber: 2.0 Consensus size: 84
1286380 TAAACTCATG
* *
1286390 TTTTATGATATTATTTTTTATTTTATCTTTAGGAATTTTAGTTTAAATAGTTTTAAGTATTTTAA
1 TTTTATGATATTATTTCTTATTTTATCTTTAGGAATTTTAGTTTAAATAATTTTAAGTATTTTAA
*
1286455 TTAGGATTTAGGATATTAT
66 TTAGGATTTAAGATATTAT
*
1286474 TTTTATTATATT-TTATCTTATATTT-TCTTTAGGAATTTTAGTTTAAATAATTTTAAGTATTTT
1 TTTTATGATATTATT-TCTTAT-TTTATCTTTAGGAATTTTAGTTTAAATAATTTTAAGTATTTT
1286537 AATTAGGATTTAAGATATTAT
64 AATTAGGATTTAAGATATTAT
1286558 TTT
1 TTT
1286561 AGGAATTATC
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
83 2 0.02
84 76 0.94
85 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (84 bp):
TTTTATGATATTATTTCTTATTTTATCTTTAGGAATTTTAGTTTAAATAATTTTAAGTATTTTAA
TTAGGATTTAAGATATTAT
Found at i:1286605 original size:84 final size:83
Alignment explanation
Indices: 1286416--1286607 Score: 212
Period size: 84 Copynumber: 2.3 Consensus size: 83
1286406 TTTATTTTAT
* * * * **
1286416 CTTTAGGAATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGGATATTATTTTTATT
1 CTTTAGGAATTTAAGTATAAATAATTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTAGG
* *
1286481 ATATTTTATCTTATATTTT
66 ATA-TTTATCTTATACTTG
* *
1286500 CTTTAGGAATTTTAGTTTAAATAATTTTAAGTATTTTAATTAGGATTTAAGATATTA-TTTTAGG
1 CTTTAGGAATTTAAGTATAAATAATTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTAGG
1286564 A-A-TTATCTT-TAGCTTG
66 ATATTTATCTTATA-CTTG
1286580 CTTTTAGGAATTTGAAGGCTATAAATAA
1 C-TTTAGGAATTT-AA-G-TATAAATAA
1286608 CTTCTCAGGG
Statistics
Matches: 95, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 2 0.02
80 10 0.11
81 11 0.12
82 2 0.02
83 7 0.07
84 63 0.66
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (83 bp):
CTTTAGGAATTTAAGTATAAATAATTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTAGG
ATATTTATCTTATACTTG
Found at i:1287116 original size:19 final size:19
Alignment explanation
Indices: 1287088--1287134 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1287078 CTTTAAATTA
*
1287088 TTTA-TTTAATTATTTTCT
1 TTTATTTTAATTATTATCT
*
1287106 TTTATTTTAATTCTTATCT
1 TTTATTTTAATTATTATCT
1287125 TTTATTTTAA
1 TTTATTTTAA
1287135 AAACAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTTTAATTATTATCT
Found at i:1287187 original size:10 final size:10
Alignment explanation
Indices: 1287172--1287243 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
1287162 TCTGTATTAC
1287172 TATTATTATT
1 TATTATTATT
1287182 TATTA-T-TT
1 TATTATTATT
*
1287190 TATTATTCTT
1 TATTATTATT
**
1287200 CCCTT-TTATT
1 -TATTATTATT
1287210 TATTATTATT
1 TATTATTATT
1287220 TATT-TTATTT
1 TATTATTA-TT
1287230 TATT-TTATT
1 TATTATTATT
1287239 ATATT
1 -TATT
1287244 TTTTCAACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.14
9 9 0.18
10 33 0.65
11 2 0.04
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (10 bp):
TATTATTATT
Found at i:1287228 original size:5 final size:5
Alignment explanation
Indices: 1287203--1287245 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
1287193 TATTCTTCCC
*
1287203 TTTTA -TTTA TTATTA -TTTA TTTTA TTTTA TTTTA TTATA TTTT
1 TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1287246 TTCAACTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 7 0.21
5 23 0.70
6 3 0.09
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:1295820 original size:28 final size:27
Alignment explanation
Indices: 1295765--1295826 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
1295755 TATGTTAATA
* *
1295765 TTATT-TTTTATAATATTTTTTAATAT
1 TTATTGTTTTATAATATATTTTAAGAT
* *
1295791 TTTTTGTTTTATAATATCATTTTACGAT
1 TTATTGTTTTATAATAT-ATTTTAAGAT
1295819 TTATTGTT
1 TTATTGTT
1295827 ATCCTGTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 4 0.14
27 11 0.38
28 14 0.48
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (27 bp):
TTATTGTTTTATAATATATTTTAAGAT
Found at i:1303247 original size:35 final size:35
Alignment explanation
Indices: 1303201--1303268 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
1303191 TTTATTAAAC
*
1303201 AAAAATTACATACATGAATTAAACGAAATTAAATA
1 AAAAATCACATACATGAATTAAACGAAATTAAATA
*
1303236 AAAAATCACATACATGAATTAAACGGAATTAAA
1 AAAAATCACATACATGAATTAAACGAAATTAAA
1303269 CCATCATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (35 bp):
AAAAATCACATACATGAATTAAACGAAATTAAATA
Found at i:1307536 original size:12 final size:13
Alignment explanation
Indices: 1307503--1307536 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1307493 TATCTTTCCC
1307503 TTCTTCTCTTAAT
1 TTCTTCTCTTAAT
1307516 TTCCTTCTCTT-AT
1 TT-CTTCTCTTAAT
1307529 TTCTTCTC
1 TTCTTCTC
1307537 CAAGTATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 6 0.30
14 8 0.40
ACGTcount: A:0.09, C:0.29, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTTCTCTTAAT
Found at i:1313446 original size:44 final size:44
Alignment explanation
Indices: 1313383--1313470 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
1313373 TTTTTTCAAC
*
1313383 GTGACTCTTTATAAAAGTGAATAGATTTTTTATATATTAAATTT
1 GTGACTCTTTATAAAAGTGAATAGATTTTTTATATATCAAATTT
1313427 GTGACTCTTTATAAAAGTGAATAGATTTTTTATATATCAAATTT
1 GTGACTCTTTATAAAAGTGAATAGATTTTTTATATATCAAATTT
1313471 ATGTAATGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (44 bp):
GTGACTCTTTATAAAAGTGAATAGATTTTTTATATATCAAATTT
Found at i:1317439 original size:222 final size:222
Alignment explanation
Indices: 1317027--1317462 Score: 604
Period size: 222 Copynumber: 2.0 Consensus size: 222
1317017 AACATACATC
* * * **
1317027 GAAAGAGCAGAAAAAGCTCCAGCTGATACAGAAGGCAGACCATGGCACCATAAGAACCGATCCAT
1 GAAAGACCAGAAAAACCTCAAGCTGATACAGAAGGCAGACCACAGCACCATAAGAACCGATCCAT
* * ** *
1317092 CACTCTCGGGTCATCTAAAGATTTCAATTTTGATTATGTTGATGGATGTGTGGAAACCGAGACAG
66 CACTCTCGGATCATCTAAAGATTTCAAGTTTGACAATGTTGATGGATGCGTGGAAACCGAGACAG
* * * * *
1317157 CGATACTGTCTGAAGCTGCAGCAGAATCTCTACTGAATAAAGCAGAAAGACAGCAAGAAGAAAAT
131 CGACACCGTCTGAAGCTGCAGCAGAAGCTCTACTGAATAAAGCAGAAAGACAGAAAGAAGAAAAC
*
1317222 GCTACTAAGATGGTAGAAATGTGCATT
196 GCTACCAAGATGGTAGAAATGTGCATT
* * **
1317249 GAAAGACCAGAAATACCTCAAGCTGATACGGAAGGCAGACCACAGCACCATAAGAGTCGATCCAT
1 GAAAGACCAGAAAAACCTCAAGCTGATACAGAAGGCAGACCACAGCACCATAAGAACCGATCCAT
* *
1317314 CACTCTCGGATCATCTAAAGATTTCAAGTTTGACAATGTTGATGTATGCGTGGAAATCGAGACAG
66 CACTCTCGGATCATCTAAAGATTTCAAGTTTGACAATGTTGATGGATGCGTGGAAACCGAGACAG
* * * *
1317379 CGACGCCGTCTGAAGCTGCAGCAGAAGCTCTA-TGGAATGAAGCAGCAAGGCAGAAAGAAGAAAA
131 CGACACCGTCTGAAGCTGCAGCAGAAGCTCTACT-GAATAAAGCAGAAAGACAGAAAGAAGAAAA
* *
1317443 CGCTACCAAGCTGGTGGAAA
195 CGCTACCAAGATGGTAGAAA
1317463 CTTACGAATG
Statistics
Matches: 185, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
221 1 0.01
222 184 0.99
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.19
Consensus pattern (222 bp):
GAAAGACCAGAAAAACCTCAAGCTGATACAGAAGGCAGACCACAGCACCATAAGAACCGATCCAT
CACTCTCGGATCATCTAAAGATTTCAAGTTTGACAATGTTGATGGATGCGTGGAAACCGAGACAG
CGACACCGTCTGAAGCTGCAGCAGAAGCTCTACTGAATAAAGCAGAAAGACAGAAAGAAGAAAAC
GCTACCAAGATGGTAGAAATGTGCATT
Found at i:1319304 original size:20 final size:21
Alignment explanation
Indices: 1319275--1319313 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1319265 TAGTATAATC
*
1319275 CTAAATTTTAAACA-TAAACT
1 CTAAACTTTAAACACTAAACT
1319295 CTAAACTTTAAACACTAAA
1 CTAAACTTTAAACACTAAA
1319314 TAATACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
CTAAACTTTAAACACTAAACT
Found at i:1322446 original size:58 final size:56
Alignment explanation
Indices: 1322308--1322547 Score: 381
Period size: 56 Copynumber: 4.2 Consensus size: 56
1322298 TACGGAAATT
* *
1322308 CACAAAATGCCCATACGGAAATTCATAAACTCATTAGGAATTTCTTAGTTTTTGCA
1 CACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCA
* *
1322364 CACAAAGTGCCCATATGGAAATTCATAAACTCATTACGAATTTCTTAGTTTTTTTGCA
1 CACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAG--TTTTTGCA
*
1322422 CACAAAGTGCCCTTACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCA
1 CACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCA
* *
1322478 CACAAAGTGCCCATGCGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCA
1 CACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCA
* *
1322534 CACACAGTTCCCAT
1 CACAAAGTGCCCAT
1322548 TTGGTAATCA
Statistics
Matches: 171, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
56 118 0.69
58 53 0.31
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.34
Consensus pattern (56 bp):
CACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCA
Found at i:1322508 original size:114 final size:112
Alignment explanation
Indices: 1322308--1322537 Score: 379
Period size: 114 Copynumber: 2.0 Consensus size: 112
1322298 TACGGAAATT
1322308 CACAAAATGCCCATACGGAAATTCATAAACTCATTAGGAATTTCTTAGTTTTTGCACACAAAGTG
1 CACAAAATGCCCATACGGAAATTCATAAACTCATTAGGAATTTCTTAGTTTTTGCACACAAAGTG
*
1322373 CCCATATGGAAATTCATAAACTCATTACGAATTTCTTAGTTTTTTTGCA
66 CCCATACGGAAATTCATAAACTCATTACGAATTTCTTAG--TTTTTGCA
* * *
1322422 CACAAAGTGCCCTTACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTG
1 CACAAAATGCCCATACGGAAATTCATAAACTCATTAGGAATTTCTTAGTTTTTGCACACAAAGTG
* * *
1322487 CCCATGCGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCA
66 CCCATACGGAAATTCATAAACTCATTACGAATTTCTTAGTTTTTGCA
1322534 CACA
1 CACA
1322538 CAGTTCCCAT
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
112 12 0.11
114 97 0.89
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (112 bp):
CACAAAATGCCCATACGGAAATTCATAAACTCATTAGGAATTTCTTAGTTTTTGCACACAAAGTG
CCCATACGGAAATTCATAAACTCATTACGAATTTCTTAGTTTTTGCA
Found at i:1323008 original size:22 final size:22
Alignment explanation
Indices: 1322957--1323012 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
1322947 TTCTGGATCC
* * *
1322957 ATGGTATCGATACTTCTCTCCT
1 ATGGTACCGATACTTCTATACT
1322979 A--GTACCGATACTTCTATACT
1 ATGGTACCGATACTTCTATACT
1322999 ATGGTACCGATACT
1 ATGGTACCGATACT
1323013 CCATTACAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 17 0.59
22 12 0.41
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (22 bp):
ATGGTACCGATACTTCTATACT
Found at i:1323026 original size:19 final size:19
Alignment explanation
Indices: 1323002--1323049 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1322992 CTATACTATG
1323002 GTACCGATACTCCATTACA
1 GTACCGATACTCCATTACA
1323021 GTACCGATACTCCATTACA
1 GTACCGATACTCCATTACA
1323040 GTACCGATAC
1 GTACCGATAC
1323050 CATTTATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.25
Consensus pattern (19 bp):
GTACCGATACTCCATTACA
Found at i:1330149 original size:14 final size:14
Alignment explanation
Indices: 1330132--1330165 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1330122 TCTTAAAAAA
1330132 TAAAAT-TTAATTTT
1 TAAAATCTT-ATTTT
1330146 TAAAATCTTATTTT
1 TAAAATCTTATTTT
1330160 TAAAAT
1 TAAAAT
1330166 ATATTGTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAAATCTTATTTT
Found at i:1331462 original size:2 final size:2
Alignment explanation
Indices: 1331453--1331489 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1331443 TATATAAAAC
*
1331453 TA TA -A TA TA TA TA TG 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
1331490 ATGTTGCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1331600 original size:2 final size:2
Alignment explanation
Indices: 1331593--1331697 Score: 160
Period size: 2 Copynumber: 53.0 Consensus size: 2
1331583 TAAGTAATAG
*
1331593 TA TA TA TA -A AA TA TA CTA 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
* *
1331635 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1331676 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
1331698 ATGTTGCACT
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
1 2 0.02
2 91 0.96
3 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1333107 original size:16 final size:16
Alignment explanation
Indices: 1333086--1333117 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1333076 CTAACATAGA
1333086 TTCATGCAGCTACAAC
1 TTCATGCAGCTACAAC
1333102 TTCATGCAGCTACAAC
1 TTCATGCAGCTACAAC
1333118 GTGAGCGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.25
Consensus pattern (16 bp):
TTCATGCAGCTACAAC
Found at i:1336461 original size:75 final size:75
Alignment explanation
Indices: 1336360--1336869 Score: 629
Period size: 74 Copynumber: 6.9 Consensus size: 75
1336350 ATTTCAAAGG
* * * * *
1336360 AACTTTCTCAAGCGAGATGAAA-TTTGTTTTAAGAAAAACAATGTCGAGTGAAATAAAATTTCTT
1 AACTGTCTCAAGCGAGA-CAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC-T
1336424 GTTTCGAGT-AA
64 GTTTCGAGTGAA
* * * * * *
1336435 AAATGTCTTAAGCGAGACAAAGTTTGTTTTAAGAAAAATAATCTAAACTTAGATAAAATTT-TGT
1 AACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTGT
*
1336499 TTAGAGTGAA
66 TTCGAGTGAA
* * * * *
1336509 AGCTGTCTCAAGCGAGACGAAGTTTGTTTTATGAAAAACAATCTTAAGTGAGATAAAATTTCCGT
1 AACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTGT
1336574 TTCGAGTGAA
66 TTCGAGTGAA
* * *
1336584 AACTGTCTCAAGAGAGACGAAGTTTGTTTTAAGAAAAACTATCTCAAGTGAGATAAAATTTCTGT
1 AACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTGT
*
1336649 TTCAAGTGAA
66 TTCGAGTGAA
* * * *
1336659 AACTATCTCAAGCAAGACGAAGTTTGTTTTAA-TAAAACAATCTCAAGTGAGATAAAATTTC-GT
1 AACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTGT
*
1336722 TTTGAGTGAA
66 TTCGAGTGAA
* * * ** *
1336732 AATTGTCTCAAGCAAGACAAAGTTTGTTTTATGAAAAAGTATCTCGAGTGAGATAAAATTTCAT-
1 AACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC-TG
1336796 TTT-GAGTGAA
65 TTTCGAGTGAA
* **
1336806 AACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACTATCTTGAGTGAGATAAAATTTCTG
1 AACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTG
1336870 ATCTTTGCTT
Statistics
Matches: 378, Mismatches: 50, Indels: 15
0.85 0.11 0.03
Matches are distributed among these distances:
73 48 0.13
74 173 0.46
75 157 0.42
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (75 bp):
AACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTGT
TTCGAGTGAA
Found at i:1336611 original size:149 final size:149
Alignment explanation
Indices: 1336360--1336867 Score: 641
Period size: 149 Copynumber: 3.4 Consensus size: 149
1336350 ATTTCAAAGG
* * * * * * *
1336360 AACTTTCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATGTCGAGTGAAATAAAATTTCTTG
1 AACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC-CG
* * * * *
1336425 TTTCGAGT-AAAAATGTCTTAAGCGAGACAAAGTTTGTTTTAAGAAAAA-TAATCTAAACTTAGA
65 TTTCGAGTGAAAAATGTCTCAAGAGAGACAAAGTTTGTTTTAAGAAAAACT-ATCTCAAGTGAGA
1336488 TAAAATTTTGTTTAGAGTGAA
129 TAAAATTTTGTTTAGAGTGAA
* * *
1336509 AGCTGTCTCAAGCGAGACGAAGTTTGTTTTATGAAAAACAATCTTAAGTGAGATAAAATTTCCGT
1 AACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCCGT
* *
1336574 TTCGAGTGAAAACTGTCTCAAGAGAGACGAAGTTTGTTTTAAGAAAAACTATCTCAAGTGAGATA
66 TTCGAGTGAAAAATGTCTCAAGAGAGACAAAGTTTGTTTTAAGAAAAACTATCTCAAGTGAGATA
1336639 AAATTTCTGTTTCA-AGTGAA
131 AAATTT-TGTTT-AGAGTGAA
* * *
1336659 AACTATCTCAAGCAAGACGAAGTTTGTTTTAA-TAAAACAATCTCAAGTGAGATAAAATTT-CGT
1 AACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCCGT
* * * * *
1336722 TTTGAGTGAAAATTGTCTCAAGCA-AGACAAAGTTTGTTTTATGAAAAAGTATCTCGAGTGAGAT
66 TTCGAGTGAAAAATGTCTCAAG-AGAGACAAAGTTTGTTTTAAGAAAAACTATCTCAAGTGAGAT
** *
1336786 AAAATTTCATTTTGAGTGAA
130 AAAATTTTGTTTAGAGTGAA
* * **
1336806 AACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACTATCTTGAGTGAGATAAAATTTC
1 AACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC
1336868 TGATCTTTGC
Statistics
Matches: 312, Mismatches: 39, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
147 38 0.12
148 99 0.32
149 134 0.43
150 40 0.13
151 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (149 bp):
AACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCCGT
TTCGAGTGAAAAATGTCTCAAGAGAGACAAAGTTTGTTTTAAGAAAAACTATCTCAAGTGAGATA
AAATTTTGTTTAGAGTGAA
Found at i:1346914 original size:13 final size:13
Alignment explanation
Indices: 1346878--1346927 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1346868 GTTTATTAGC
*
1346878 ATTTATATTTAATT
1 ATTTAT-TTTTATT
* *
1346892 ATATAGTTTTATT
1 ATTTATTTTTATT
*
1346905 ATTTATTTTTCTT
1 ATTTATTTTTATT
1346918 ATTTATTTTT
1 ATTTATTTTT
1346928 TTCTTGATCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (13 bp):
ATTTATTTTTATT
Found at i:1347001 original size:28 final size:30
Alignment explanation
Indices: 1346976--1347030 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1346966 ATGTTTATAT
1346976 TCTATAT-TACTACT-ATATTTTATTATTA
1 TCTATATGTACTACTAATATTTTATTATTA
**
1347004 TCTATATGTACTTTTAATATTTTATTA
1 TCTATATGTACTACTAATATTTTATTA
1347031 CTATATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 7 0.30
29 5 0.22
30 11 0.48
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (30 bp):
TCTATATGTACTACTAATATTTTATTATTA
Found at i:1357728 original size:49 final size:52
Alignment explanation
Indices: 1357656--1357753 Score: 132
Period size: 49 Copynumber: 1.9 Consensus size: 52
1357646 AATACTTCGC
*
1357656 TTAGGATGAAAACCCAAAGGGGCGTCCT-AAGT-AAAAAAAT-GAAAAACGT
1 TTAGGATGAAAACCCAAAGGGGCGCCCTAAAGTGAAAAAAATCGAAAAACGT
* *
1357705 TTAGGGTGAAAACCCGAAA-GGGCGCCCTAAATTGAAAAAAATCGAAAAA
1 TTAGGATGAAAACCC-AAAGGGGCGCCCTAAAGTGAAAAAAATCGAAAAA
1357754 AGAAAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 22 0.52
50 6 0.14
51 8 0.19
52 6 0.14
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.15
Consensus pattern (52 bp):
TTAGGATGAAAACCCAAAGGGGCGCCCTAAAGTGAAAAAAATCGAAAAACGT
Found at i:1358674 original size:105 final size:104
Alignment explanation
Indices: 1358522--1358829 Score: 380
Period size: 98 Copynumber: 3.0 Consensus size: 104
1358512 TCGTGCCACT
* * * * **
1358522 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAATAATTTCCCAGTT
1 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAA-AATTTCCCAGTT
*
1358587 TCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
65 TCAGGGCCAATCTCAACTTCACAGCGAAGGATATTGGACC
*
1358627 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAAC-AAA-----CAATTT
1 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAAATTTCCCAGTTT
*
1358686 C-GGAGCCAATCTCAACTTCACAACGAAGGATATTGGACC
66 CAGG-GCCAATCTCAACTTCACAGCGAAGGATATTGGACC
* * *
1358725 CAAGACAGCACAAGCTCAACTTCGCAGCGAAGGGGCGGCTGACTGTCAATAAACAATTTCCCGGT
1 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAA-CAA-AATTTCCCAGT
* **
1358790 TCCAGAACCAATCTCAACTTCACAGC-AGAGGATATTGGAC
64 TTCAGGGCCAATCTCAACTTCACAGCGA-AGGATATTGGAC
1358830 TCAGAACAAT
Statistics
Matches: 175, Mismatches: 17, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
97 2 0.01
98 87 0.50
100 1 0.01
101 2 0.01
103 2 0.01
104 1 0.01
105 45 0.26
106 34 0.19
107 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (104 bp):
CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAAATTTCCCAGTTT
CAGGGCCAATCTCAACTTCACAGCGAAGGATATTGGACC
Found at i:1360343 original size:13 final size:13
Alignment explanation
Indices: 1360307--1360356 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1360297 GTTTATTAGC
*
1360307 ATTTATATTTAATT
1 ATTTAT-TTTTATT
* *
1360321 ATATAGTTTTATT
1 ATTTATTTTTATT
*
1360334 ATTTATTTTTCTT
1 ATTTATTTTTATT
1360347 ATTTATTTTT
1 ATTTATTTTT
1360357 TTCTTGATCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (13 bp):
ATTTATTTTTATT
Found at i:1360430 original size:28 final size:30
Alignment explanation
Indices: 1360405--1360459 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1360395 ATGTTTATAT
1360405 TCTATAT-TACTACT-ATATTTTATTATTA
1 TCTATATGTACTACTAATATTTTATTATTA
**
1360433 TCTATATGTACTTTTAATATTTTATTA
1 TCTATATGTACTACTAATATTTTATTA
1360460 CTATATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 7 0.30
29 5 0.22
30 11 0.48
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (30 bp):
TCTATATGTACTACTAATATTTTATTATTA
Found at i:1361676 original size:41 final size:41
Alignment explanation
Indices: 1361615--1361852 Score: 196
Period size: 41 Copynumber: 5.7 Consensus size: 41
1361605 GGTTCATCAA
*
1361615 TAGTGGCGTTATTTCA-ACAAACGCCGCAAAAGAGTAGTACTT
1 TAGTGGCGTT-TTT-ATACAAACGCCGCAAAAGACTAGTACTT
** * * *
1361657 TAGTGGCGTTTTTATACAAACGCCGTTATACAC-ATGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCAAAAGACTA-GTACTT
* *
1361698 TAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCA-TACTT
1 TAGTGGCGTTT-T-TATACAAACGCCGCAAAAGACT-AGTACTT
* * **
1361741 TAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCAAAAGACTAGTACTT
* * * * * *
1361782 TAGTGGCATTTTTATTCAAACGCCGTTATAA-ACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCG-CAAAAGACTAGTACTT
*
1361823 TAGTGGCGTTTGTGTTTACAAACGCCGCAA
1 TAGTGGCGTTT-T-TATACAAACGCCGCAA
1361853 GTTTACAAAT
Statistics
Matches: 157, Mismatches: 29, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
40 2 0.01
41 95 0.61
42 16 0.10
43 43 0.27
45 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCAAAAGACTAGTACTT
Found at i:1361780 original size:84 final size:84
Alignment explanation
Indices: 1361631--1361850 Score: 225
Period size: 84 Copynumber: 2.6 Consensus size: 84
1361621 CGTTATTTCA
* * * *
1361631 ACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGTTATACACATGTAC
1 ACAAACGCCGCAAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAACACACGTAC
1361696 TATAGTGGCGTTTGTGTTT
66 TATAGTGGCGTTTGTGTTT
* * * *
1361715 ACAAACGCCGCTAAAGACTCA-TACTTTAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTA
1 ACAAACGCCGCAAAAGACT-AGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAACACACGTA
* *
1361779 CTTTAGTGGCATTT-T-TATT
65 CTATAGTGGCGTTTGTGT-TT
* * * * *
1361798 -CAAACGCCGTTATAA-ACTTGTACTATAGTGGCGTTTGTGTTTACAAACGCCGC
1 ACAAACGCCG-CAAAAGACTAGTACTTTAGTGGCGTTT-T-TATACAAACGCCGC
1361851 AAGTTTACAA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
82 28 0.25
83 6 0.05
84 78 0.69
85 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (84 bp):
ACAAACGCCGCAAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAACACACGTAC
TATAGTGGCGTTTGTGTTT
Found at i:1361780 original size:125 final size:126
Alignment explanation
Indices: 1361615--1361850 Score: 370
Period size: 125 Copynumber: 1.9 Consensus size: 126
1361605 GGTTCATCAA
*
1361615 TAGTGGCGTTATTTCAACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGC
1 TAGTGGCGTTATTTCAACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCATTTTTATACAAACGC
*
1361680 CGTTATACACATGTACTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATACTT
66 CGTTATAAACATGTACTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATACTT
* * * *
1361741 TAGTGGCGTT-TTT-ATACAAACTCCGCTAAAGACG-CGTACTTTAGTGGCATTTTTATTCAAAC
1 TAGTGGCGTTATTTCA-ACAAACGCCGCAAAAGA-GTAGTACTTTAGTGGCATTTTTATACAAAC
*
1361803 GCCGTTATAAACTTGTACTATAGTGGCGTTTGTGTTTACAAACGCCGC
64 GCCGTTATAAACATGTACTATAGTGGCGTTTGTGTTTACAAACGCCGC
1361851 AAGTTTACAA
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
124 1 0.01
125 89 0.88
126 11 0.11
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (126 bp):
TAGTGGCGTTATTTCAACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCATTTTTATACAAACGC
CGTTATAAACATGTACTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATACTT
Found at i:1365307 original size:85 final size:86
Alignment explanation
Indices: 1365128--1365447 Score: 328
Period size: 85 Copynumber: 3.7 Consensus size: 86
1365118 AGGTAATTAG
* * * *
1365128 CGGCGTTTGTATCCAAAAACGCCGCTATAGGTATGACTTTTTGCGGCATTTGAGTTC-ACAAACG
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGTATTT--GTTCTAAAAACG
* * *
1365192 CCGTTATAGGTCTGAC-CTTTTG
64 CCGCTATAGGTCTAACTCTTTTA
* * * * * *
1365214 CGGCGTTTGTGTCCAAAACCGCCGCTATAGGTCTGACCTTTTGTGGTGTTTGTTCTAAAAACGCC
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGTATTTGTTCTAAAAACGCC
*
1365279 AG-TATAGGTCT-TCTCTTTTA
66 -GCTATAGGTCTAACTCTTTTA
* * * * * *
1365299 CGGTGTTTGTATCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGTATTTTTTCTAGAAACGCT
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGTATTTGTTCTAAAAACGCC
**
1365364 GCTATATATCATAACT-TTTTA
66 GCTATAGGTC-TAACTCTTTTA
* * *
1365385 CGGCGTTTAT-TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGTGTTTGTTCAAAAAACG
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATAT-GACCTTTTGCGGTATTTGTTCTAAAAACG
1365448 TCGTAATAGA
Statistics
Matches: 196, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
84 6 0.03
85 104 0.53
86 84 0.43
87 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (86 bp):
CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGTATTTGTTCTAAAAACGCC
GCTATAGGTCTAACTCTTTTA
Found at i:1365457 original size:43 final size:42
Alignment explanation
Indices: 1365127--1365473 Score: 243
Period size: 43 Copynumber: 8.1 Consensus size: 42
1365117 AAGGTAATTA
* * * *
1365127 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTATGACTTTTT
1 GCGGTGTTTGT-TCAAAAAACGCCGCTATAGATATGACCTTTT
** * * * *
1365170 GCGGCATTTGAGTTC-ACAAACGCCGTTATAGGTCTGACCTTTT
1 GCGGTGTTT--GTTCAAAAAACGCCGCTATAGATATGACCTTTT
* * * * *
1365213 GCGGCGTTTGTGTCCAAAACCGCCGCTATAGGTCTGACCTTTT
1 GCGGTGTTTGT-TCAAAAAACGCCGCTATAGATATGACCTTTT
* * * * *
1365256 GTGGTGTTTGTTCTAAAAACGCCAG-TATAGGTCT-TCTCTTTT
1 GCGGTGTTTGTTCAAAAAACGCC-GCTATAGATATGAC-CTTTT
* *
1365298 ACGGTGTTTGTATCAAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGTGTTTGT-TCAAAAAACGCCGCTATAGATATGACCTTTT
* * * * * * * *
1365341 GCGGTATTTTTTCTAGAAACGCTGCTATATATCATAACTTTTT
1 GCGGTGTTTGTTCAAAAAACGCCGCTATAGAT-ATGACCTTTT
* * * *
1365384 ACGGCGTTTATTCCAAAAACGCCGCTATAGATATCGACCTTTT
1 GCGGTGTTTGTTCAAAAAACGCCGCTATAGATAT-GACCTTTT
* *
1365427 GCGGTGTTTGTTCAAAAAACGTCG-TAATAGATATTGACCTATT
1 GCGGTGTTTGTTCAAAAAACGCCGCT-ATAGATA-TGACCTTTT
1365470 GCGG
1 GCGG
1365474 CATTTTTTGT
Statistics
Matches: 246, Mismatches: 45, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
41 3 0.01
42 56 0.23
43 181 0.74
44 4 0.02
45 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
GCGGTGTTTGTTCAAAAAACGCCGCTATAGATATGACCTTTT
Found at i:1366121 original size:20 final size:21
Alignment explanation
Indices: 1366078--1366121 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1366068 TCATTAGGGG
*
1366078 TGAACAAAACTCGACTCGACT
1 TGAACAAAACTCGACTCGAAT
*
1366099 TGAA-AAAACTCGACTCTAAT
1 TGAACAAAACTCGACTCGAAT
1366119 TGA
1 TGA
1366122 CTTCGTGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (21 bp):
TGAACAAAACTCGACTCGAAT
Found at i:1367057 original size:31 final size:31
Alignment explanation
Indices: 1367022--1367103 Score: 94
Period size: 33 Copynumber: 2.6 Consensus size: 31
1367012 AAATGATAGA
**
1367022 GAATTTTTCAGTGATATAT-TTTGTCATTTCT
1 GAATTTTTCAGTGATATATCACT-TCATTTCT
*
1367053 GAATTTTTTTAGTTGATATATCACTTCATTTCT
1 GAA-TTTTTCAG-TGATATATCACTTCATTTCT
*
1367086 GAACTTTTCAGTGATATA
1 GAATTTTTCAGTGATATA
1367104 CCAGACACTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 10 0.23
32 13 0.30
33 19 0.44
34 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.51
Consensus pattern (31 bp):
GAATTTTTCAGTGATATATCACTTCATTTCT
Found at i:1368099 original size:26 final size:26
Alignment explanation
Indices: 1368066--1368115 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1368056 TAATGTAATT
1368066 AGGAGTTAATGCTTCTAATATAATGC
1 AGGAGTTAATGCTTCTAATATAATGC
* *
1368092 AGGAGTTAATGTTTCTAATGTAAT
1 AGGAGTTAATGCTTCTAATATAAT
1368116 AATGTATGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (26 bp):
AGGAGTTAATGCTTCTAATATAATGC
Found at i:1374462 original size:85 final size:85
Alignment explanation
Indices: 1374359--1374527 Score: 232
Period size: 85 Copynumber: 2.0 Consensus size: 85
1374349 CATGAGTACC
* *
1374359 GATACCAAATTTGGCTTCGATGTTTTCAAAAATGCCTCAATATCGATACTAACCCTT-TGAGTAT
1 GATACCAAATTTGACTTCGATGTTTTCAAAAATACCTCAATATCGATACTAA-CCTTCTGAGTAT
*
1374423 CGATACTGGAACCTGAGTATT
65 CAATACTGGAACCTGAGTATT
* * * * * *
1374444 GATACCAAATTTGACTTCGATGTTTTCATAAATACTTCAGTATCGATATTGACCTTCTGAGTATT
1 GATACCAAATTTGACTTCGATGTTTTCAAAAATACCTCAATATCGATACTAACCTTCTGAGTATC
*
1374509 AATACTGGACCCTGAGTAT
66 AATACTGGAACCTGAGTAT
1374528 CTGTAACACC
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 4 0.05
85 69 0.95
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (85 bp):
GATACCAAATTTGACTTCGATGTTTTCAAAAATACCTCAATATCGATACTAACCTTCTGAGTATC
AATACTGGAACCTGAGTATT
Found at i:1375148 original size:54 final size:54
Alignment explanation
Indices: 1375024--1375352 Score: 493
Period size: 54 Copynumber: 6.1 Consensus size: 54
1375014 TTACACACGT
* * * ** *
1375024 AGTGCCAATACGGTAATTCACAAACTCATTATGAATTACGTGGAGTTGCACACAT
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTC-TTAAGTTGCACACAC
*
1375079 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
*
1375133 AGTGCCAATATGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
* * *
1375187 AGTGCCAATAC--ATAATTCATAAACTTATTATGAATATCTTAAGTTGCACACAT
1 AGTGCCAATACGGA-AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
*
1375240 AATGCCAATACGGAAATTCATAAACTCATTATG-ATTTCTTAAGTTGCACACAC
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
* *
1375293 AGTGCCAATACGTAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
1375347 AGTGCC
1 AGTGCC
1375353 CATTCGGTAA
Statistics
Matches: 250, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
52 1 0.00
53 95 0.38
54 118 0.47
55 36 0.14
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (54 bp):
AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
Found at i:1375237 original size:107 final size:107
Alignment explanation
Indices: 1375024--1375352 Score: 509
Period size: 107 Copynumber: 3.1 Consensus size: 107
1375014 TTACACACGT
* * * ** *
1375024 AGTGCCAATACGGTAATTCACAAACTCATTATGAATTACGTGGAGTTGCACACATAGTGCCAATA
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTC-TTAAGTTGCACACACAGTGCCAATA
1375089 CGGA-AATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
65 C--ATAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
*
1375133 AGTGCCAATATGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
* *
1375198 ATAATTCATAAACTTATTATGAATATCTTAAGTTGCACACAT
66 ATAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
*
1375240 AATGCCAATACGGAAATTCATAAACTCATTATG-ATTTCTTAAGTTGCACACACAGTGCCAATAC
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
*
1375304 GTAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
66 AT-AATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
1375347 AGTGCC
1 AGTGCC
1375353 CATTCGGTAA
Statistics
Matches: 203, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
106 33 0.16
107 112 0.55
108 23 0.11
109 35 0.17
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (107 bp):
AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
ATAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
Found at i:1379441 original size:95 final size:94
Alignment explanation
Indices: 1379264--1379443 Score: 211
Period size: 95 Copynumber: 1.9 Consensus size: 94
1379254 ACAAAGGGAA
* * * ** * *
1379264 GTATCGATACCATGGATCCAGAATGTCAAAATGGTACTGATACTGAAAAGGAGTATCGGTATCAT
1 GTATCGATACCATGCAACCAGAATATCAAAATGGTACTGATACTGAAAAGGAAAATCGATACCAT
* *
1379329 AGTATAGTAGCATCGATACTGAGATAAGG
66 AGTATAGAAGCAACGATACTGAGATAAGG
* *
1379358 GTATCGATACCATGCAACACAGAATAT-AGAAATGGTA-TCGATATTGAAAGGGAAAATCGATAC
1 GTATCGATACCATGCAAC-CAGAATATCA-AAATGGTACT-GATACTGAAAAGGAAAATCGATAC
*
1379421 CATAGTATAGAAGTAACGATACT
63 CATAGTATAGAAGCAACGATACT
1379444 AGGGTAGTAG
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
94 18 0.25
95 53 0.75
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.24
Consensus pattern (94 bp):
GTATCGATACCATGCAACCAGAATATCAAAATGGTACTGATACTGAAAAGGAAAATCGATACCAT
AGTATAGAAGCAACGATACTGAGATAAGG
Found at i:1379928 original size:45 final size:45
Alignment explanation
Indices: 1379851--1379939 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
1379841 AAACCGAATC
* * * * * *
1379851 CATAATTAAAGTGTATGAACATATGCATTAAGGCGTGAAAGGATT
1 CATAATTAAAGTGCATAAACAGACGCACTAAGGCATGAAAGGATT
* *
1379896 CATAATTAAAGTGCATAAACGGACGCACTAAGGTATGAAAGGAT
1 CATAATTAAAGTGCATAAACAGACGCACTAAGGCATGAAAGGAT
1379940 GCCATAACTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (45 bp):
CATAATTAAAGTGCATAAACAGACGCACTAAGGCATGAAAGGATT
Found at i:1380013 original size:26 final size:26
Alignment explanation
Indices: 1379930--1380085 Score: 120
Period size: 26 Copynumber: 6.5 Consensus size: 26
1379920 GCACTAAGGT
* *
1379930 ATGAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAATTAAAGTGC
* * *
1379956 GTGAACGAATG---T-ATT-AAG-GC
1 ATGAAAGGATGCCATAATTAAAGTGC
* *
1379976 ATGAAAGAATGCCATAATTGAAGTGC
1 ATGAAAGGATGCCATAATTAAAGTGC
* *
1380002 ATGAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAATTAAAGTGC
*
1380028 ATGAACGGATG-C---ATT-AAG-GC
1 ATGAAAGGATGCCATAATTAAAGTGC
*
1380048 ATGAAAGGATGTCATAATTAAAGTGC
1 ATGAAAGGATGCCATAATTAAAGTGC
*
1380074 ATGAACGGATGC
1 ATGAAAGGATGC
1380086 AGTAAGGTAA
Statistics
Matches: 101, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
20 23 0.23
21 5 0.05
22 4 0.04
23 2 0.02
24 6 0.06
25 7 0.07
26 54 0.53
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (26 bp):
ATGAAAGGATGCCATAATTAAAGTGC
Found at i:1380014 original size:72 final size:72
Alignment explanation
Indices: 1379930--1380085 Score: 249
Period size: 72 Copynumber: 2.2 Consensus size: 72
1379920 GCACTAAGGT
* *
1379930 ATGAAAGGATGCCATAACTAAAATGCGTGAACGAATGTATTAAGGCATGAAAGAATGCCATAATT
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGAATGCATTAAGGCATGAAAGAATGCCATAATT
*
1379995 GAAGTGC
66 AAAGTGC
* * *
1380002 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGTCATAATT
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGAATGCATTAAGGCATGAAAGAATGCCATAATT
1380067 AAAGTGC
66 AAAGTGC
*
1380074 ATGAACGGATGC
1 ATGAAAGGATGC
1380086 AGTAAGGTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (72 bp):
ATGAAAGGATGCCATAACTAAAATGCATGAACGAATGCATTAAGGCATGAAAGAATGCCATAATT
AAAGTGC
Found at i:1380075 original size:46 final size:46
Alignment explanation
Indices: 1380000--1380394 Score: 574
Period size: 46 Copynumber: 8.6 Consensus size: 46
1379990 TAATTGAAGT
1380000 GCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
* * * *
1380046 GCATGAAAGGATGTCATAATTAAAGTGCATGAACGGATGCAGTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
* * *
1380092 GTAAGAAAGGATGCCATAACTAAAATGCATGAACGGATGCAGTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
*
1380138 GTATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
** * * ** * *
1380184 GCATGAAACAATGTCATAATTAAAGCGTATGAACGGATGCACTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
* *
1380230 GCATGAAAGGATGCCATAACTAAAATACATGAACGGGTGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
** * *
1380276 GTGTGAAAGGATGCCATAATTAAAATGCATGAACGGATGCACTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
*
1380322 GCATGAAAGGATGCCATAACTAAAATGCATGAACGAATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
*
1380368 GCATGAAAGGATGTCATAACTAAAATG
1 GCATGAAAGGATGCCATAACTAAAATG
1380395 TAAGAACAAC
Statistics
Matches: 307, Mismatches: 42, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 307 1.00
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAG
Found at i:1380106 original size:118 final size:118
Alignment explanation
Indices: 1379886--1380131 Score: 296
Period size: 118 Copynumber: 2.1 Consensus size: 118
1379876 CATTAAGGCG
* * * *
1379886 TGAAAGGAT-TCATAATTAAAGTGCATAAACGGACGCACTAAGGTATGAAAGGATGCCATAACTA
1 TGAAAGGATGCCATAACTAAAATGCATAAACGGACGCACTAAGGCATGAAAGGATGCCATAACTA
* * * * * * *
1379950 AAATGCGTGAACGAATGTATTAAGGCATGAAAGAATGCCATAATTGAAGTGCA
66 AAATGCATGAACGAATGCAGTAAGGCAAGAAAGAATGCCATAACTAAAATGCA
* * * * *
1380003 TGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGTCATAATTA
1 TGAAAGGATGCCATAACTAAAATGCATAAACGGACGCACTAAGGCATGAAAGGATGCCATAACTA
* * * *
1380068 AAGTGCATGAACGGATGCAGTAAGGTAAGAAAGGATGCCATAACTAAAATGCA
66 AAATGCATGAACGAATGCAGTAAGGCAAGAAAGAATGCCATAACTAAAATGCA
*
1380121 TGAACGGATGC
1 TGAAAGGATGC
1380132 AGTAAGGTAT
Statistics
Matches: 107, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
117 9 0.08
118 98 0.92
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.21
Consensus pattern (118 bp):
TGAAAGGATGCCATAACTAAAATGCATAAACGGACGCACTAAGGCATGAAAGGATGCCATAACTA
AAATGCATGAACGAATGCAGTAAGGCAAGAAAGAATGCCATAACTAAAATGCA
Found at i:1380146 original size:164 final size:163
Alignment explanation
Indices: 1379850--1380177 Score: 467
Period size: 164 Copynumber: 2.0 Consensus size: 163
1379840 TAAACCGAAT
* * * * *
1379850 CCATAATTAAAGTGTATGAACATATGCATTAAGGCGTGAAAGGATTCATAATTAAAGTGCATAAA
1 CCATAACTAAAATGCATGAACAGATGCATTAAGGCATGAAAGGATTCATAATTAAAGTGCATAAA
* * * *
1379915 CGGACGCACTAAGGTATGAAAGGATGCCATAACTAAAATGCGTGAACGAATGTATTAAGGCATGA
66 CGGACGCACTAAGGTAAGAAAGGATGCCATAACTAAAATGCATGAACGAATGCAGTAAGGCATGA
* * *
1379980 AAGAATGCCATAATTGAAGTGCATGAAAGGATG
131 AAGAATGCCATAACTAAAATGCATGAAAGGATG
* *
1380013 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAGTGCATGA
1 CCATAACTAAAATGCATGAACAGATGCATTAAGGCATGAAAGGAT-TCATAATTAAAGTGCATAA
* * * *
1380078 ACGGATGCAGTAAGGTAAGAAAGGATGCCATAACTAAAATGCATGAACGGATGCAGTAAGGTATG
65 ACGGACGCACTAAGGTAAGAAAGGATGCCATAACTAAAATGCATGAACGAATGCAGTAAGGCATG
* *
1380143 AAAGGATGCCATAACTAAAATGCATGAACGGATG
130 AAAGAATGCCATAACTAAAATGCATGAAAGGATG
1380177 C
1 C
1380178 ATTAAGGCAT
Statistics
Matches: 144, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
163 39 0.27
164 105 0.73
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (163 bp):
CCATAACTAAAATGCATGAACAGATGCATTAAGGCATGAAAGGATTCATAATTAAAGTGCATAAA
CGGACGCACTAAGGTAAGAAAGGATGCCATAACTAAAATGCATGAACGAATGCAGTAAGGCATGA
AAGAATGCCATAACTAAAATGCATGAAAGGATG
Found at i:1386373 original size:46 final size:46
Alignment explanation
Indices: 1386242--1386378 Score: 168
Period size: 46 Copynumber: 3.0 Consensus size: 46
1386232 TACCGAATCT
* * *
1386242 ATAATTAAAGTGCATGAACGGATGTATTAAGGAATAAAAGGATGTC
1 ATAATTAAAGTGCATGAACGGATGCATTAAGGAATGAAAGGATGAC
* *
1386288 ATAATTAAAGTGCATCAACGGATGCACTAAGGTAA-GAAAGGATGAC
1 ATAATTAAAGTGCATGAACGGATGCATTAAGG-AATGAAAGGATGAC
* * * * *
1386334 ATAACTAAAATGCGTGAACGGATGCATTAAGGCATGAAAGAATGA
1 ATAATTAAAGTGCATGAACGGATGCATTAAGGAATGAAAGGATGA
1386379 TACACTTGAT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
45 1 0.01
46 74 0.96
47 2 0.03
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (46 bp):
ATAATTAAAGTGCATGAACGGATGCATTAAGGAATGAAAGGATGAC
Found at i:1394700 original size:23 final size:23
Alignment explanation
Indices: 1394627--1394706 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
1394617 GTCAAAATTG
* *
1394627 CCACATAGATTTGTCTCGAAGGA
1 CCACATAGAATTGTCCCGAAGGA
** * * *
1394650 CCATGTAGAATTTATCCTGAAGGG
1 CCACATAGAA-TTGTCCCGAAGGA
1394674 CCACATAGAATTGTCCCGAAGGA
1 CCACATAGAATTGTCCCGAAGGA
*
1394697 CCACGTAGAA
1 CCACATAGAA
1394707 CCCTCGACTC
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
23 26 0.60
24 17 0.40
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.23
Consensus pattern (23 bp):
CCACATAGAATTGTCCCGAAGGA
Found at i:1394862 original size:15 final size:15
Alignment explanation
Indices: 1394809--1394875 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 15
1394799 AGTATTTTTT
*
1394809 ATTCAGATATAACAC
1 ATTCACATATAACAC
* *
1394824 ATTCACATA-GA-AT
1 ATTCACATATAACAC
* *
1394837 TTTCACGTATAACAC
1 ATTCACATATAACAC
*
1394852 ATTCACATATAACAT
1 ATTCACATATAACAC
*
1394867 GTTCACATA
1 ATTCACATA
1394876 CTAATCAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
13 8 0.21
14 2 0.05
15 29 0.74
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (15 bp):
ATTCACATATAACAC
Found at i:1397706 original size:8 final size:10
Alignment explanation
Indices: 1397667--1397705 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
1397657 TCAGTTTCAC
*
1397667 CCTTCTTTCT
1 CCTTCTCTCT
1397677 CCTTCTCTCT
1 CCTTCTCTCT
1397687 CCTTCTCTCT
1 CCTTCTCTCT
1397697 CCTTCTCTC
1 CCTTCTCTC
1397706 CCTACCCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (10 bp):
CCTTCTCTCT
Found at i:1405738 original size:17 final size:18
Alignment explanation
Indices: 1405716--1405754 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1405706 ACTTCTTGTT
1405716 TATTATTTA-CATTATAA
1 TATTATTTATCATTATAA
*
1405733 TATTATTTATTATTATAA
1 TATTATTTATCATTATAA
1405751 -ATTA
1 TATTA
1405755 AATTTATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATTTATCATTATAA
Found at i:1406869 original size:30 final size:29
Alignment explanation
Indices: 1406835--1406907 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
1406825 GTTCAAACCA
*
1406835 GTTTTGCCGGTTTTCAGCCGGTTCATCCCG
1 GTTTTGCCGGTTTTCAGCCGGTTC-TACCG
* * *
1406865 GTTTTACCGATTTTCAGTCGGTTCTACCG
1 GTTTTGCCGGTTTTCAGCCGGTTCTACCG
1406894 GTTTTCAGCCGGTT
1 GTTTT--GCCGGTT
1406908 CATTGCCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 9 0.26
30 21 0.60
31 5 0.14
ACGTcount: A:0.10, C:0.26, G:0.25, T:0.40
Consensus pattern (29 bp):
GTTTTGCCGGTTTTCAGCCGGTTCTACCG
Found at i:1406892 original size:20 final size:20
Alignment explanation
Indices: 1406862--1406908 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1406852 CCGGTTCATC
*
1406862 CCGGTTTTACCGATTTTCAG
1 CCGGTTCTACCGATTTTCAG
* *
1406882 TCGGTTCTACCGGTTTTCAG
1 CCGGTTCTACCGATTTTCAG
1406902 CCGGTTC
1 CCGGTTC
1406909 ATTGCCAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.28, G:0.23, T:0.38
Consensus pattern (20 bp):
CCGGTTCTACCGATTTTCAG
Found at i:1407231 original size:19 final size:19
Alignment explanation
Indices: 1407207--1407243 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1407197 ATGACCAACA
*
1407207 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1407226 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1407244 CATTATCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1407354 original size:20 final size:20
Alignment explanation
Indices: 1407329--1407381 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1407319 GATTTTAGAT
*
1407329 AATCGCAATGTGAATATGTA
1 AATCGCAATGCGAATATGTA
1407349 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
*
1407369 AATCGCAACGCGA
1 AATCGCAATGCGA
1407382 TAACACGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:1407396 original size:21 final size:19
Alignment explanation
Indices: 1407370--1407496 Score: 85
Period size: 20 Copynumber: 6.3 Consensus size: 19
1407360 GAATATGTAA
1407370 ATCGCAACGCGATAAC-ACGT
1 ATCGCAACGCGAT-ACGAC-T
*
1407390 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATAC-GACT
* *
1407411 ATCACAACGCGATTCGGACT
1 ATCGCAACGCGATAC-GACT
**
1407431 ATCGCAACGCGATAATACGT
1 ATCGCAACGCGATACGAC-T
* *
1407451 GATCGCAACGGGATTCTGACT
1 -ATCGCAACGCGATAC-GACT
* *
1407472 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAC-GACT
1407492 ATCGC
1 ATCGC
1407497 GTTGTGATAA
Statistics
Matches: 89, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
19 2 0.02
20 56 0.63
21 27 0.30
22 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (19 bp):
ATCGCAACGCGATACGACT
Found at i:1407420 original size:20 final size:20
Alignment explanation
Indices: 1407391--1407496 Score: 133
Period size: 20 Copynumber: 5.2 Consensus size: 20
1407381 ATAACACGTG
1407391 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
1407411 ATCACAACGCGATTCGGACT
1 ATCGCAACGCGATTCTGACT
**
1407431 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
*
1407451 GATCGCAACGGGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
1407472 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1407492 ATCGC
1 ATCGC
1407497 GTTGTGATAA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 55 0.75
21 14 0.19
22 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1407508 original size:61 final size:61
Alignment explanation
Indices: 1407370--1407496 Score: 209
Period size: 61 Copynumber: 2.1 Consensus size: 61
1407360 GAATATGTAA
* *
1407370 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACTATCACAACGCGATTCGGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCACAACGAGATTCGGACT
* * *
1407431 ATCGCAACGCGATAATACGTGATCGCAACGGGATTCTGACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCACAACGAGATTCGGACT
1407492 ATCGC
1 ATCGC
1407497 GTTGTGATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (61 bp):
ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCACAACGAGATTCGGACT
Found at i:1407517 original size:61 final size:61
Alignment explanation
Indices: 1407370--1407526 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
1407360 GAATATGTAA
* *** *
1407370 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACTATCACAACGCGATTCGGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACTATCACAACGAGATTCGGACT
*** * * *
1407431 ATCGCAACGCGATAATACGTGATCGCAACGGGATTCTGACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACTATCACAACGAGATTCGGACT
*** * * *
1407492 ATCGCGTTGTGATAATATAAAATCGCAATGCGATT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATT
1407527 TTCAAAGCGC
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 81 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (61 bp):
ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACTATCACAACGAGATTCGGACT
Found at i:1407691 original size:22 final size:22
Alignment explanation
Indices: 1407659--1407735 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
1407649 TCACTCTCTA
*
1407659 CGGCGAAATCCGTCCCCATTTT
1 CGGCGAAATCCGTCCCCATCTT
*
1407681 CGGTGAAATCCGTCCCCATCTT
1 CGGCGAAATCCGTCCCCATCTT
*
1407703 CGGCGAAATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTT
1407725 CGGCGAAATCC
1 CGGCGAAATCC
1407736 ATCTATTTCC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.22
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTT
Found at i:1408158 original size:35 final size:33
Alignment explanation
Indices: 1408079--1408161 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
1408069 CAACGACAAA
*
1408079 ATTT-GTGTTGCGATTATCTCGTTGCGATAGCC
1 ATTTCGTGTTGCGATTATCTCGTTGCGATAACC
* *
1408111 ATTTCGCGTTGCGATTATCTCGTTGCGATAATC
1 ATTTCGTGTTGCGATTATCTCGTTGCGATAACC
1408144 AGTTTTCGTGTTGCGATT
1 A--TTTCGTGTTGCGATT
1408162 TTCATTTTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 4 0.09
33 26 0.59
35 14 0.32
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (33 bp):
ATTTCGTGTTGCGATTATCTCGTTGCGATAACC
Found at i:1408171 original size:20 final size:21
Alignment explanation
Indices: 1408132--1408189 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
1408122 CGATTATCTC
**
1408132 GTTGCGATAATCAGTTTTCGT
1 GTTGCGATTTTCAGTTTTCGT
1408153 GTTGCGATTTTCA-TTTTCGT
1 GTTGCGATTTTCAGTTTTCGT
*
1408173 GTTGCGATTTTAAGTTT
1 GTTGCGATTTTCAGTTT
1408190 CAGAAACTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.16, C:0.12, G:0.22, T:0.50
Consensus pattern (21 bp):
GTTGCGATTTTCAGTTTTCGT
Found at i:1410166 original size:20 final size:20
Alignment explanation
Indices: 1410141--1410326 Score: 204
Period size: 20 Copynumber: 9.6 Consensus size: 20
1410131 AGAAGAATAG
* *
1410141 TCGCAACACGAAAATGATTA
1 TCGCAACGCGAAAATGACTA
**
1410161 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
**
1410181 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
**
1410201 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
1410221 TCGCAACG-G--GAT-A--A
1 TCGCAACGCGAAAATGACTA
*
1410235 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
1410255 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
1410275 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
1410295 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
1410315 TCGCAACGCGAA
1 TCGCAACGCGAA
1410327 TTTAGTTTCG
Statistics
Matches: 143, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
14 8 0.06
15 1 0.01
16 1 0.01
17 3 0.02
18 1 0.01
19 1 0.01
20 128 0.90
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1410203 original size:40 final size:39
Alignment explanation
Indices: 1410141--1410329 Score: 235
Period size: 40 Copynumber: 4.9 Consensus size: 39
1410131 AGAAGAATAG
* *
1410141 TCGCAACACGAAAATGATTATCGCAACGCGAATTTGACTA
1 TCGCAACGCG-AAATGACTATCGCAACGCGAATTTGACTA
*
1410181 TCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTA
1 TCGCAACGCGAA-ATGACTATCGCAACGCGAATTTGACTA
* * **
1410221 TCGCAACG-G-GAT-A--ATCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAATGACTATCGCAACGCGAATTTGACTA
1410255 TCGCAACGCGGAAATGACTATCGCAACGCGAATTTGACTA
1 TCGCAACGC-GAAATGACTATCGCAACGCGAATTTGACTA
*
1410295 TCGCAATGCGAAAATGACTATCGCAACGCGAATTT
1 TCGCAACGCG-AAATGACTATCGCAACGCGAATTT
1410330 AGTTTCGCGT
Statistics
Matches: 128, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
34 26 0.20
36 2 0.02
37 3 0.02
38 1 0.01
39 4 0.03
40 92 0.72
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (39 bp):
TCGCAACGCGAAATGACTATCGCAACGCGAATTTGACTA
Found at i:1410281 original size:74 final size:74
Alignment explanation
Indices: 1410160--1410300 Score: 230
Period size: 74 Copynumber: 1.9 Consensus size: 74
1410150 GAAAATGATT
** *
1410160 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGACTATCGC
1410225 AACGGGATA
66 AACGGGATA
*
1410234 ATCGCAATGCGAAAATGACTATCGCAACGCGGAA-ATGACTATCGCAACGCGAATTTGACTATCG
1 ATCGCAACGCGAAAATGACTATCGCAACGC-GAATATGACTATCGCAACGCGAATTTGACTATCG
1410298 CAA
65 CAA
1410301 TGCGAAAATG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 59 0.95
75 3 0.05
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (74 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGACTATCGC
AACGGGATA
Found at i:1410306 original size:94 final size:94
Alignment explanation
Indices: 1410149--1410322 Score: 287
Period size: 94 Copynumber: 1.9 Consensus size: 94
1410139 AGTCGCAACA
* * *
1410149 CGAAAATGATTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAAT
1 CGAAAATGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGACTATCGCAACGCGAAA
*
1410214 TTGACTATCGCAACGGGATAATCGCAATG
66 ATGACTATCGCAACGGGATAATCGCAATG
*
1410243 CGAAAATGACTATCGCAACGCGGAA-ATGACTATCGCAACGCGAATTTGACTATCGCAATGCGAA
1 CGAAAATGACTATCGCAACGC-GAATATGACTATCGCAACGCGAATTTGACTATCGCAACGCGAA
1410307 AATGACTATCGCAACG
65 AATGACTATCGCAACG
1410323 CGAATTTAGT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
94 71 0.96
95 3 0.04
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (94 bp):
CGAAAATGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGACTATCGCAACGCGAAA
ATGACTATCGCAACGGGATAATCGCAATG
Found at i:1410344 original size:19 final size:19
Alignment explanation
Indices: 1410322--1410363 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1410312 CTATCGCAAC
*
1410322 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCACGTT
* *
1410341 GCGATTTTGGTTTCACGTT
1 GCGAATTTAGTTTCACGTT
1410360 GCGA
1 GCGA
1410364 TAGTCATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.17, G:0.29, T:0.40
Consensus pattern (19 bp):
GCGAATTTAGTTTCACGTT
Found at i:1410447 original size:20 final size:20
Alignment explanation
Indices: 1410405--1410467 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1410395 GATAGTCAAA
* ** *
1410405 TTCGCGTTGCGATAATAATT
1 TTCGTGTTGCGATTTTAAGT
1410425 TTCGTGTTGCGATTTTAAGT
1 TTCGTGTTGCGATTTTAAGT
*
1410445 TTCGTATTGCGATTTTAAGT
1 TTCGTGTTGCGATTTTAAGT
1410465 TTC
1 TTC
1410468 AGAAACTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.19, C:0.13, G:0.21, T:0.48
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTAAGT
Found at i:1411020 original size:21 final size:21
Alignment explanation
Indices: 1410951--1411054 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 21
1410941 CACATGTCAT
* * *
1410951 CGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCCCCTCCCAC
**
1410972 CGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGCCCCTCCCA-C
* *
1410994 C-CTCAAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
* *
1411014 CGTTCAAGAGGCCCC-CGTCAT
1 CGTTCAAGAGGCCCCTC-CCAC
* *
1411035 CGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCCCTCCCA
1411055 ACATTCTAGA
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
20 3 0.05
21 58 0.92
22 2 0.03
ACGTcount: A:0.20, C:0.39, G:0.19, T:0.21
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:1411035 original size:42 final size:42
Alignment explanation
Indices: 1410954--1411054 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
1410944 ATGTCATCGT
* * * *
1410954 TCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCCATCATCCC
* * **
1410996 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCCGTCATCGT
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCCATCATCCC
* *
1411038 TGAAGAGGTCCCTCCCA
1 TCAAGAGGCCCCTCCCA
1411055 ACATTCTAGA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (42 bp):
TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCCATCATCCC
Found at i:1412460 original size:30 final size:30
Alignment explanation
Indices: 1412426--1412491 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
1412416 ATAAGAGTTG
* *
1412426 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTAATGTGTAAATAATTATT
1412456 ATTTGTTTAATTAATGTGTAAATAATTATT
1 ATTTGTTTAATTAATGTGTAAATAATTATT
1412486 ATTTGT
1 ATTTGT
1412492 GCTTGTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTAATGTGTAAATAATTATT
Found at i:1412668 original size:34 final size:34
Alignment explanation
Indices: 1412608--1412743 Score: 121
Period size: 34 Copynumber: 3.9 Consensus size: 34
1412598 ATCATATTCG
* * * *
1412608 CGTTGCGATAGTCTAATACACTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* * *
1412642 CGTTGCGATAGTCAAATTCCCATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCT
* *
1412682 CGTTGCGATAGTC-ATTTCGCGTTGCGATTATCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
*
1412715 CGTTGTGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT
1412744 AGTTAAATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
33 14 0.17
34 39 0.47
36 1 0.01
37 1 0.01
39 12 0.14
40 16 0.19
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:1412725 original size:73 final size:73
Alignment explanation
Indices: 1412598--1412783 Score: 246
Period size: 73 Copynumber: 2.5 Consensus size: 73
1412588 TTCAATCTGC
* * * * * *
1412598 ATCATATTCGCGTTGCGATAGTCTAATACACTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCC
1 ATCAAATTCGCGTTGCGATAGTC-ATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCCC
1412663 ATTGCGATA
65 ATTGCGATA
* * *
1412672 ATCAAATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGTGATAGTCAAATTCGCG
1 ATCAAATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCCCA
1412737 TTGCGATA
66 TTGCGATA
* * *
1412745 GTTAAATTCGCGTTGCGATAGTCATTTTAGCGTTGCGAT
1 ATCAAATTCGCGTTGCGATAGTCA-TTTCGCGTTGCGAT
1412784 AGTCATTTTC
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
73 64 0.65
74 35 0.35
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (73 bp):
ATCAAATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCCCA
TTGCGATA
Found at i:1412744 original size:20 final size:20
Alignment explanation
Indices: 1412642--1412899 Score: 176
Period size: 20 Copynumber: 13.8 Consensus size: 20
1412632 GCGATTTTCT
*
1412642 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
1412662 CATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1412682 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
1412701 CGTTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
*
1412715 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1412735 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
** *
1412755 CGTTGCGATAGTCATTTTAG
1 CGTTGCGATAGTCAAATTCG
**
1412775 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
1412795 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
** *
1412809 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCAAATTCG
* *
1412829 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
1412843 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
1412863 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
1412883 TGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
1412900 GAATGTGTAA
Statistics
Matches: 185, Mismatches: 35, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
14 29 0.16
16 3 0.02
17 1 0.01
18 2 0.01
19 16 0.09
20 134 0.72
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1412818 original size:34 final size:34
Alignment explanation
Indices: 1412775--1412852 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
1412765 GTCATTTTAG
1412775 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
*
1412809 CGTTGCGATAGTCATTTTTGCATTGCGATTATCC
1 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1412843 CGTTGCGATA
1 CGTTGCGATA
1412853 TTCAAATTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
Found at i:1412869 original size:34 final size:34
Alignment explanation
Indices: 1412775--1412871 Score: 113
Period size: 34 Copynumber: 2.9 Consensus size: 34
1412765 GTCATTTTAG
** *
1412775 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCACATTGCGATTATCC
** **
1412809 CGTTGCGATAGTCATTTTTGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCACATTGCGATTATCC
* *
1412843 CGTTGCGATATTCAAATTCACGTTGCGAT
1 CGTTGCGATAGTCAAATTCACATTGCGAT
1412872 AGTCATATTC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCACATTGCGATTATCC
Found at i:1413097 original size:18 final size:18
Alignment explanation
Indices: 1413074--1413108 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1413064 AAGCCGGTTG
*
1413074 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1413092 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1413109 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1415164 original size:14 final size:14
Alignment explanation
Indices: 1415145--1415181 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1415135 TCCCGTGGCA
1415145 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
1415159 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
1415173 TTCTTCTTC
1 TT-TTCTTC
1415182 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1415405 original size:24 final size:24
Alignment explanation
Indices: 1415371--1415424 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1415361 CTGAAACATC
1415371 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1415395 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1415419 ATCAAA
1 ATCAAA
1415425 TTTCGAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1416276 original size:20 final size:20
Alignment explanation
Indices: 1416246--1416372 Score: 175
Period size: 20 Copynumber: 6.3 Consensus size: 20
1416236 AATTCAGTGA
* *
1416246 TGCGTTAGTCAGAATCACGT
1 TGCGATAGTCAGAATCGCGT
*
1416266 TGTGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
*
1416286 TGCGATAGTCAGAATCTCGT
1 TGCGATAGTCAGAATCGCGT
1416306 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
**
1416326 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
1416347 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
1416367 TGCGAT
1 TGCGAT
1416373 CACGTGTTAT
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 75 0.80
21 15 0.16
22 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:1416345 original size:21 final size:21
Alignment explanation
Indices: 1416319--1416393 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
1416309 GATAGTCAGA
1416319 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCACGTATT
**
1416340 ATCGCGTTGCGAT-A-GTCAGA
1 ATCGCGTTGCGATCACGT-ATT
*
1416360 ATCGCGTTGCGATCACGTGTT
1 ATCGCGTTGCGATCACGTATT
*
1416381 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1416394 TTACATATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
21 26 0.58
22 2 0.04
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.31
Consensus pattern (21 bp):
ATCGCGTTGCGATCACGTATT
Found at i:1416360 original size:41 final size:41
Alignment explanation
Indices: 1416263--1416393 Score: 185
Period size: 41 Copynumber: 3.2 Consensus size: 41
1416253 GTCAGAATCA
* ** *
1416263 CGTTGTGATAGTCAGAATCGCGTTGCGAT-A-GTCAGAATCT
1 CGTTGCGATAGTCAGAATCGCGTTGCGATCACGT-ATTATCG
1416303 CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCG
1 CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCG
*
1416344 CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTGTTATCG
1 CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCG
*
1416385 CATTGCGAT
1 CGTTGCGAT
1416394 TTACATATTC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
40 28 0.34
41 53 0.64
42 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (41 bp):
CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCG
Found at i:1416407 original size:20 final size:20
Alignment explanation
Indices: 1416382--1416430 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1416372 TCACGTGTTA
1416382 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1416402 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1416422 TCGCATTGC
1 TCGCATTGC
1416431 AATTATCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1416485 original size:20 final size:21
Alignment explanation
Indices: 1416439--1416487 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1416429 GCAATTATCT
*
1416439 AAAATCGCAATGCGGATTTCG
1 AAAATCGCAATGCGGATGTCG
1416460 AAAATCGCAATGC-GATGGTC-
1 AAAATCGCAATGCGGAT-GTCG
1416480 AAAATCGC
1 AAAATCGC
1416488 GTTGCGAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (21 bp):
AAAATCGCAATGCGGATGTCG
Found at i:1416532 original size:20 final size:19
Alignment explanation
Indices: 1416508--1416554 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1416498 TGGAAACTGA
*
1416508 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
1416528 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
1416547 ATTGCGAT
1 ATTGCGAT
1416555 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:1416544 original size:19 final size:19
Alignment explanation
Indices: 1416520--1416556 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1416510 TGCGATAATG
*
1416520 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1416539 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1416557 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1417265 original size:31 final size:31
Alignment explanation
Indices: 1417224--1417284 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1417214 TGACCGCACC
** *
1417224 TTAATAAAATAAAAATGAACATGATCAAATT
1 TTAATAAAATAAAAACAAAAATGATCAAATT
*
1417255 TTAATGAAATAAAAACAAAAATGATCAAAT
1 TTAATAAAATAAAAACAAAAATGATCAAAT
1417285 ATTATGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.26
Consensus pattern (31 bp):
TTAATAAAATAAAAACAAAAATGATCAAATT
Found at i:1422179 original size:29 final size:29
Alignment explanation
Indices: 1422123--1422264 Score: 94
Period size: 29 Copynumber: 4.9 Consensus size: 29
1422113 TAATATGGCC
* * *
1422123 AAAATAGAAACTTAAAGAACTAGAATAGAA
1 AAAATAGAAACTT-AGGGACTAAAATAGAA
* *
1422153 AAAATAGAAACTTAGGGATTAAAATAGTA
1 AAAATAGAAACTTAGGGACTAAAATAGAA
** * **
1422182 ATTATAGAAAGTTAAAGGGA-TAAAA-ATTA
1 AAAATAGAAACTT--AGGGACTAAAATAGAA
* * *
1422211 AAAACAGAAACCTCAAGGACTAAAAT--AA
1 AAAATAGAAA-CTTAGGGACTAAAATAGAA
*
1422239 AAAATAGAATCTTAGGGACTAAAATA
1 AAAATAGAAACTTAGGGACTAAAATA
1422265 AATAAAACAA
Statistics
Matches: 86, Mismatches: 20, Indels: 14
0.72 0.17 0.12
Matches are distributed among these distances:
27 13 0.15
28 13 0.15
29 36 0.42
30 19 0.22
31 5 0.06
ACGTcount: A:0.58, C:0.07, G:0.15, T:0.20
Consensus pattern (29 bp):
AAAATAGAAACTTAGGGACTAAAATAGAA
Found at i:1423602 original size:3 final size:3
Alignment explanation
Indices: 1423594--1423626 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1423584 AAAAATAAGC
*
1423594 ATA ATA ATA ATA ATA ATA ATA A-A ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1423627 AAAATGACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:1424018 original size:134 final size:133
Alignment explanation
Indices: 1423779--1424031 Score: 404
Period size: 134 Copynumber: 1.9 Consensus size: 133
1423769 TGGTGTGGAC
*
1423779 GACACTGCTCATACGTGATGAAGAGTTCGGATCGTCTATAGGAAGGGTGATAACTCAGTTCCTAC
1 GACACTGCTCATACGTGATGAAGAGTTCGGATCATCTATAGGAAGGGTGATAACTCAGTTCCTAC
1423844 GCGATGAGGACAGTTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTATGGTCGGG
66 GCGATGAGGACAGTTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTATGGTCGGG
1423909 GAT
131 GAT
* **
1423912 GACACTGCTCATACGTGATGAAGAGTTCTTG-TCCATC-ATTAGGAAGGGTGATAACTTGGTTCC
1 GACACTGCTCATACGTGATGAAGAGTTC-GGAT-CATCTA-TAGGAAGGGTGATAACTCAGTTCC
*
1423975 TACGCGATGAGGAC-GTCTGGTTATCTATGGGTGACACGGCTCCTACGTGATGAGGAG
63 TACGCGATGAGGACAGT-TGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAG
1424032 ATCTGTTTCA
Statistics
Matches: 111, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
133 32 0.29
134 79 0.71
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (133 bp):
GACACTGCTCATACGTGATGAAGAGTTCGGATCATCTATAGGAAGGGTGATAACTCAGTTCCTAC
GCGATGAGGACAGTTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTATGGTCGGG
GAT
Found at i:1424065 original size:134 final size:134
Alignment explanation
Indices: 1423817--1424065 Score: 313
Period size: 134 Copynumber: 1.9 Consensus size: 134
1423807 GGATCGTCTA
1423817 TAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACAGTTGGTTATCTAAGGGTGACACGGCT
1 TAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACAGTTGGTTATCTAAGGGTGACACGGCT
* ** * ** ** * * *
1423882 CCTACGTGATGAGGAGGTATGGTCGGGGATGACACTGCTCATACGTGATGAAGAGTTCTTGTCCA
66 CCTACGTGATGAGGAGATATGGTCAAGAAAAACACAACTAAAACATGATGAAGAGTTCTTGTCCA
1423947 TCAT
131 TCAT
** *
1423951 TAGGAAGGGTGATAACTTGGTTCCTACGCGATGAGGAC-GTCTGGTTATCTATGGGTGACACGGC
1 TAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACAGT-TGGTTATCTAAGGGTGACACGGC
* * *
1424015 TCCTACGTGATGAGGAGATCTGTTTCAAGAAAAACA-AACTAAAATATGATG
65 TCCTACGTGATGAGGAGATATG-GTCAAGAAAAACACAACTAAAACATGATG
1424066 TGTTTCAAAA
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
133 2 0.02
134 87 0.91
135 7 0.07
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (134 bp):
TAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACAGTTGGTTATCTAAGGGTGACACGGCT
CCTACGTGATGAGGAGATATGGTCAAGAAAAACACAACTAAAACATGATGAAGAGTTCTTGTCCA
TCAT
Found at i:1425176 original size:2 final size:2
Alignment explanation
Indices: 1425169--1425197 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1425159 GATGTATGTA
1425169 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1425198 ATGTATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1425819 original size:2 final size:2
Alignment explanation
Indices: 1425812--1425874 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1425802 GCTTTATTGT
1425812 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1425854 AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC A
1425875 TATATATATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.