Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 23
Found at i:2698701 original size:15 final size:15
Alignment explanation
Indices: 2698681--2698710 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2698671 TGCTATATAT
*
2698681 GTCCCGTAGGACTAC
1 GTCCCGAAGGACTAC
2698696 GTCCCGAAGGACTAC
1 GTCCCGAAGGACTAC
2698711 AATACCCTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.17
Consensus pattern (15 bp):
GTCCCGAAGGACTAC
Found at i:2701295 original size:16 final size:17
Alignment explanation
Indices: 2701276--2701317 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2701266 TTTAAATACA
2701276 ATTTAATTAAAATA-AT
1 ATTTAATTAAAATATAT
* * *
2701292 ATTTCATTCAAATATTT
1 ATTTAATTAAAATATAT
2701309 ATTTAATTA
1 ATTTAATTA
2701318 TCGAGTAATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAAATATAT
Found at i:2705191 original size:15 final size:16
Alignment explanation
Indices: 2705157--2705193 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2705147 TGAAACATAT
2705157 ATATATATTTTAAAATA
1 ATAT-TATTTTAAAATA
2705174 ATATTATTTTAAAA-A
1 ATATTATTTTAAAATA
2705189 ATATT
1 ATATT
2705194 TAAGATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 10 0.50
17 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTATTTTAAAATA
Found at i:2706541 original size:77 final size:77
Alignment explanation
Indices: 2706414--2706567 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
2706404 TTTTTAATTG
2706414 CTTAGATATGTGTTCTGACCATTTTTCAAGTGTCTTGAACTTGTATTTATATGTTGGAATGAAAT
1 CTTAGATATGTGTTCTGACCATTTTTCAAGTGTCTTGAACTTGTATTTATATGTTGGAATGAAAT
2706479 TGTGGTTGTTTC
66 TGTGGTTGTTTC
2706491 CTTAGATATGTGTTCTGACCATTTTTCAAGTGTCTTGAACTTGTATTTATATGTTGGAATGAAAT
1 CTTAGATATGTGTTCTGACCATTTTTCAAGTGTCTTGAACTTGTATTTATATGTTGGAATGAAAT
2706556 TGTGGTTGTTTC
66 TGTGGTTGTTTC
2706568 TAACCGTTGG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.47
Consensus pattern (77 bp):
CTTAGATATGTGTTCTGACCATTTTTCAAGTGTCTTGAACTTGTATTTATATGTTGGAATGAAAT
TGTGGTTGTTTC
Found at i:2715530 original size:122 final size:122
Alignment explanation
Indices: 2715306--2715558 Score: 389
Period size: 122 Copynumber: 2.1 Consensus size: 122
2715296 TCGATACAAG
* *
2715306 TCGATACTTGTCGTGACATAAGTATTGAAGCACATTTAACATTTTAGGTAGCAATCGAATATGTT
1 TCGATACTTGTCGTGAAATAAGTATTGAAGCACATTTAACATTTTAGGTAGCAATCGAAAATGTT
** * * *
2715371 TTCGAAGATATAACATTTTAGGTTGGACTTGATAACATTTTAGGTTGCAACTAAGTA
66 ACCAAAGATATAACATTTTAGGTTGGAATGGATAACATTTTAGGTTGCAACTAAGTA
* * * *
2715428 TTGATATTTGTCGTGAAATAAGTATTGAATCACATTTAACATTTTAGGTTGCAATCGAAAATGTT
1 TCGATACTTGTCGTGAAATAAGTATTGAAGCACATTTAACATTTTAGGTAGCAATCGAAAATGTT
* *
2715493 ACCAAAGATATAACATTTTATGTTGGAATGGATAACATTTTAGGTTGTAACTAAGTA
66 ACCAAAGATATAACATTTTAGGTTGGAATGGATAACATTTTAGGTTGCAACTAAGTA
2715550 TCGATACTT
1 TCGATACTT
2715559 AGTTAGGTAT
Statistics
Matches: 116, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
122 116 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (122 bp):
TCGATACTTGTCGTGAAATAAGTATTGAAGCACATTTAACATTTTAGGTAGCAATCGAAAATGTT
ACCAAAGATATAACATTTTAGGTTGGAATGGATAACATTTTAGGTTGCAACTAAGTA
Found at i:2716613 original size:99 final size:99
Alignment explanation
Indices: 2716441--2716643 Score: 388
Period size: 99 Copynumber: 2.1 Consensus size: 99
2716431 GATTACACAA
2716441 AGATCTTACAAGGAAAATATTAAAAAATCTAACCAAATAAACTTAAATAAAGATAGATACGGACA
1 AGATCTTACAAGGAAAATATTAAAAAATCTAACCAAATAAACTTAAATAAAGATAGATACGGACA
2716506 AATCTATTTGCATCGACAAACTAATCACAAAAGG
66 AATCTATTTGCATCGACAAACTAATCACAAAAGG
*
2716540 GGATCTTACAAGGAAAATATTAAAAAATCTAACCAAATAAACTTAAATAAAGATAGATACGGACA
1 AGATCTTACAAGGAAAATATTAAAAAATCTAACCAAATAAACTTAAATAAAGATAGATACGGACA
*
2716605 AATCTATTTGTATCGACAAACTAATCACAAAAGG
66 AATCTATTTGCATCGACAAACTAATCACAAAAGG
2716639 AGATC
1 AGATC
2716644 AAACTACTAA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.23
Consensus pattern (99 bp):
AGATCTTACAAGGAAAATATTAAAAAATCTAACCAAATAAACTTAAATAAAGATAGATACGGACA
AATCTATTTGCATCGACAAACTAATCACAAAAGG
Found at i:2717661 original size:60 final size:60
Alignment explanation
Indices: 2717585--2717766 Score: 197
Period size: 60 Copynumber: 3.0 Consensus size: 60
2717575 GTATCATATG
* * * * *
2717585 TCCTTAAACTACGATTTTCATTTTAAATT-GATCTTTAAATTTTTTAATATTCTAATTTCA
1 TCCTTAAACTATGATTTTCATTCTAAATTAG-TCTTTAAAATTTTGAATATTCCAATTTCA
* *
2717645 TCTTTAAACTATGATTTTCATTCTAAATTAGTCTTTAAAATTTTGAATATTCCAATTTGA
1 TCCTTAAACTATGATTTTCATTCTAAATTAGTCTTTAAAATTTTGAATATTCCAATTTCA
*** * * * * * *
2717705 TCCTTAAACTATGACCATCATTCT-AATTGGTCCTTAAACTTTTGAATTTTTCAATTTTA
1 TCCTTAAACTATGATTTTCATTCTAAATTAGTCTTTAAAATTTTGAATATTCCAATTTCA
2717764 TCC
1 TCC
2717767 ATGGTTATCC
Statistics
Matches: 104, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
59 32 0.31
60 71 0.68
61 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.48
Consensus pattern (60 bp):
TCCTTAAACTATGATTTTCATTCTAAATTAGTCTTTAAAATTTTGAATATTCCAATTTCA
Found at i:2717680 original size:31 final size:31
Alignment explanation
Indices: 2717588--2717683 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 31
2717578 TCATATGTCC
* *
2717588 TTAAACTACGATTTTCATTTTAAATT-GATCT
1 TTAAACTATGATTTTCATTCTAAATTAG-TCT
* *
2717619 TTAAA-T-T--TTTTAATATTCTAATTTCA-TCT
1 TTAAACTATGATTTT--CATTCTAAATT-AGTCT
2717648 TTAAACTATGATTTTCATTCTAAATTAGTCT
1 TTAAACTATGATTTTCATTCTAAATTAGTCT
2717679 TTAAA
1 TTAAA
2717684 ATTTTGAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
27 4 0.08
29 16 0.32
30 3 0.06
31 23 0.46
33 4 0.08
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (31 bp):
TTAAACTATGATTTTCATTCTAAATTAGTCT
Found at i:2741031 original size:29 final size:28
Alignment explanation
Indices: 2740984--2741048 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
2740974 TTTACGTCCA
2740984 ATTA-ATTTAGTCATATATCCTAACTTG
1 ATTAGATTTAGTCATATATCCTAACTTG
* * *
2741011 ATTTAGATTTAGTCATTTATCTTCACTTG
1 A-TTAGATTTAGTCATATATCCTAACTTG
2741040 ATTAGATTT
1 ATTAGATTT
2741049 TTAAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 11 0.33
29 21 0.64
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (28 bp):
ATTAGATTTAGTCATATATCCTAACTTG
Found at i:2745546 original size:19 final size:19
Alignment explanation
Indices: 2745522--2745590 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
2745512 GTATAGTTTG
*
2745522 TTTTTTTTTCTTTCTCTGT
1 TTTTTTTTTCTGTCTCTGT
2745541 TTTTTTTTTCTGTCTCTGT
1 TTTTTTTTTCTGTCTCTGT
* * **
2745560 CTCTAGTTTCTGTCTCTGCT
1 TTTTTTTTTCTGTCTCTG-T
2745580 TTTTTTTTTCT
1 TTTTTTTTTCT
2745591 TTCGCAGGTA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 32 0.80
20 8 0.20
ACGTcount: A:0.01, C:0.19, G:0.09, T:0.71
Consensus pattern (19 bp):
TTTTTTTTTCTGTCTCTGT
Found at i:2745946 original size:3 final size:3
Alignment explanation
Indices: 2745938--2746037 Score: 112
Period size: 3 Copynumber: 32.7 Consensus size: 3
2745928 GGCCCGTTTG
* * *
2745938 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAAA TAA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA
* * *
2745985 TTA TAA TTA TAA TAA TAA TAA TTA 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
2746033 TAA TA
1 TAA TA
2746038 TTTAAATGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.02
3 73 0.89
4 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2746623 original size:227 final size:226
Alignment explanation
Indices: 2746287--2746921 Score: 1058
Period size: 227 Copynumber: 2.8 Consensus size: 226
2746277 TCTTGATGAG
* *
2746287 TTCTTCTCATTATGAACTTCTTCCTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTCT
*
2746352 CTGGCAATGATAATCCATTAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATG
63 CTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATG
*
2746417 AATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTTTGGCAATGATAATCCA
128 AATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCA
2746482 TCAAG-TGATGAATTCAAACAAAAGGTTGAACAAA
193 T-AAGATGATGAATTCAAACAAAAGGTTGAACAAA
*
2746516 TTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CT
* **
2746581 GGCAATGATAATCCATC-AGATGATGGATTTGAACAAAAGGTTGAACAAATTCTTCTCATTATGA
65 GGCAATGATAATCCATCAAG-TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGA
* *
2746645 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGTAATGATAATCCAT
129 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCAT
* * **
2746710 TAGATGATGGATTTGAACAAAAGGTTGAACAAA
194 AAGATGATGAATTCAAACAAAAGGTTGAACAAA
*
2746743 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
2746808 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAT
66 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAT
*
2746873 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTTCTGG
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG
2746922 AAAAGCTGAT
Statistics
Matches: 381, Mismatches: 21, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
226 138 0.36
227 209 0.55
229 34 0.09
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (226 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAT
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATAA
GATGATGAATTCAAACAAAAGGTTGAACAAA
Found at i:2746944 original size:113 final size:113
Alignment explanation
Indices: 2746287--2746921 Score: 1051
Period size: 113 Copynumber: 5.6 Consensus size: 113
2746277 TCTTGATGAG
* *
2746287 TTCTTCTCATTATGAACTTCTTCCTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTCT
*
2746352 CTGGCAATGATAATCCATTAAGTGATGAATTCAAACAAAAGGTTGAACAAA
63 CTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
* *
2746403 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTTTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
2746468 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
66 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
*
2746516 TTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CT
* **
2746581 GGCAATGATAATCCATC-AGATGATGGATTTGAACAAAAGGTTGAACAAA
65 GGCAATGATAATCCATCAAG-TGATGAATTCAAACAAAAGGTTGAACAAA
2746630 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * **
2746695 GTAATGATAATCCAT-TAGATGATGGATTTGAACAAAAGGTTGAACAAA
66 GCAATGATAATCCATCAAG-TGATGAATTCAAACAAAAGGTTGAACAAA
*
2746743 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
2746808 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
66 GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
2746856 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTT-TCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTTCTCT
2746920 GG
65 GG
2746922 AAAAGCTGAT
Statistics
Matches: 494, Mismatches: 20, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
113 349 0.71
114 110 0.22
116 35 0.07
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (113 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
Found at i:2747376 original size:22 final size:22
Alignment explanation
Indices: 2747351--2747405 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
2747341 CATAAAGTTT
*
2747351 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
2747373 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
2747395 CCATCTTTGAA
1 TCATCTTTGAA
2747406 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2750075 original size:83 final size:83
Alignment explanation
Indices: 2749973--2750154 Score: 294
Period size: 83 Copynumber: 2.2 Consensus size: 83
2749963 CTTATTTCTA
* * *
2749973 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-TCCAACCAGATTAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCT-AAACCAAATCAGATAACTCAA
2750037 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
2750056 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTCTGCTAAACCAAATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAAATCAGATAACTCAAA
2750121 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
2750139 CTATGAGCACATTCAT
1 CTATGAGCAAATTCAT
2750155 TTGTTCCATT
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
83 90 0.99
84 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAAATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:2752408 original size:10 final size:10
Alignment explanation
Indices: 2752393--2752431 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2752383 TCGATTTTCC
2752393 TTTTTCTTTT
1 TTTTTCTTTT
2752403 TTTTTCTTTT
1 TTTTTCTTTT
* *
2752413 TTCTTCTTCT
1 TTTTTCTTTT
*
2752423 TCTTTCTTT
1 TTTTTCTTT
2752432 GCTGGATGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:2754408 original size:27 final size:27
Alignment explanation
Indices: 2754378--2754433 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
2754368 GTAATTATGT
*
2754378 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGCAAATACAAACGTA
* * *
2754405 AAAAATGCAAATGCAAATTCAAATGTA
1 AAAAATGAAAATGCAAATACAAACGTA
2754432 AA
1 AA
2754434 TATGTGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGCAAATACAAACGTA
Found at i:2754527 original size:7 final size:7
Alignment explanation
Indices: 2754493--2754534 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2754483 ATAAAAGTAT
2754493 AAATGCA
1 AAATGCA
* *
2754500 CAATGAA
1 AAATGCA
2754507 AAATGCA
1 AAATGCA
2754514 AAGATGCA
1 AA-ATGCA
2754522 AAATGC-
1 AAATGCA
2754528 AAATGCA
1 AAATGCA
2754535 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:2755933 original size:13 final size:15
Alignment explanation
Indices: 2755911--2755947 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2755901 TTTGACATAA
2755911 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
2755923 AAATAAAATACTTGC
1 AAATAAAATACTTGC
2755938 AAATAAAATA
1 AAATAAAATA
2755948 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:2755986 original size:18 final size:17
Alignment explanation
Indices: 2755938--2755988 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
2755928 AAATACTTGC
*
2755938 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
2755956 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
2755974 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
2755989 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:2757607 original size:19 final size:19
Alignment explanation
Indices: 2757583--2757652 Score: 86
Period size: 19 Copynumber: 3.6 Consensus size: 19
2757573 TGGTATAGTT
*
2757583 TGTTTTTTTTTTCTTTCTC
1 TGTTTTTTTTTTCTGTCTC
2757602 TGTTTTTTTTTTCTGTCTC
1 TGTTTTTTTTTTCTGTCTC
* * **
2757621 TGTCTCTAGTTTCTGTCTC
1 TGTTTTTTTTTTCTGTCTC
2757640 TGCTTTTTTTTTT
1 TG-TTTTTTTTTT
2757653 TCTTTCGCAG
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 35 0.85
20 6 0.15
ACGTcount: A:0.01, C:0.17, G:0.10, T:0.71
Consensus pattern (19 bp):
TGTTTTTTTTTTCTGTCTC
Found at i:2758011 original size:3 final size:3
Alignment explanation
Indices: 2758003--2758096 Score: 109
Period size: 3 Copynumber: 30.7 Consensus size: 3
2757993 GGCCCGTTTG
* * *
2758003 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAAA TAA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA
* *
2758050 TTA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2758097 TTTAAATGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
2 2 0.03
3 69 0.88
4 7 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2758922 original size:16 final size:16
Alignment explanation
Indices: 2758901--2758947 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
2758891 TACTGGGAGA
2758901 CTCACCCACGAAAATT
1 CTCACCCACGAAAATT
2758917 CTCACCCACGAAAATT
1 CTCACCCACGAAAATT
*
2758933 CTCACACACGAAAAT
1 CTCACCCACGAAAAT
2758948 CAGATGTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.40, C:0.36, G:0.06, T:0.17
Consensus pattern (16 bp):
CTCACCCACGAAAATT
Found at i:2762765 original size:31 final size:31
Alignment explanation
Indices: 2762730--2762942 Score: 243
Period size: 31 Copynumber: 6.9 Consensus size: 31
2762720 GAAGGACCAA
* *
2762730 TCCATATGTTCCAAAGAACATAGGTAATCAG
1 TCCATATGTCCCGAAGAACATAGGTAATCAG
* * *
2762761 TCCATATGTCTCGAAGAACATAGGTAAACAA
1 TCCATATGTCCCGAAGAACATAGGTAATCAG
*
2762792 TCCATATGTCTCGAAGAACATAGGTAAAT-AG
1 TCCATATGTCCCGAAGAACATAGGT-AATCAG
* *
2762823 TCCATATGTCCCGAAAAACATAGGTGAA-CAA
1 TCCATATGTCCCGAAGAACATAGGT-AATCAG
*
2762854 TCCAAATGTCCCGAAGAACATAGGTAAGT-AG
1 TCCATATGTCCCGAAGAACATAGGTAA-TCAG
** * * *
2762885 AACATAGGTCCCGAAGAACATAGGAAAACAG
1 TCCATATGTCCCGAAGAACATAGGTAATCAG
*
2762916 TCCATATGTCCCGAAGAAAATAGGTAA
1 TCCATATGTCCCGAAGAACATAGGTAA
2762943 CCCTCGACCC
Statistics
Matches: 152, Mismatches: 25, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
30 2 0.01
31 148 0.97
32 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAATCAG
Found at i:2762825 original size:62 final size:62
Alignment explanation
Indices: 2762727--2762942 Score: 290
Period size: 62 Copynumber: 3.5 Consensus size: 62
2762717 CCCGAAGGAC
* * *
2762727 CAATCCATATGTTCCAAAGAACATAGGT-AATCAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAATCCATATGTCCCGAAGAACATAGGTAAAT-AGTCCATATGTCCCGAAGAACATAGGTAAA
* * *
2762789 CAATCCATATGTCTCGAAGAACATAGGTAAATAGTCCATATGTCCCGAAAAACATAGGTGAA
1 CAATCCATATGTCCCGAAGAACATAGGTAAATAGTCCATATGTCCCGAAGAACATAGGTAAA
* * ** * *
2762851 CAATCCAAATGTCCCGAAGAACATAGGTAAGTAGAACATAGGTCCCGAAGAACATAGGAAAA
1 CAATCCATATGTCCCGAAGAACATAGGTAAATAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
2762913 CAGTCCATATGTCCCGAAGAAAATAGGTAA
1 CAATCCATATGTCCCGAAGAACATAGGTAA
2762943 CCCTCGACCC
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
62 132 0.98
63 3 0.02
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (62 bp):
CAATCCATATGTCCCGAAGAACATAGGTAAATAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2762904 original size:16 final size:16
Alignment explanation
Indices: 2762861--2762908 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
2762851 CAATCCAAAT
2762861 GTCCCGAAGAACATAG
1 GTCCCGAAGAACATAG
** *
2762877 GT-AAGTAGAACATAG
1 GTCCCGAAGAACATAG
2762892 GTCCCGAAGAACATAG
1 GTCCCGAAGAACATAG
2762908 G
1 G
2762909 AAAACAGTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.15
Consensus pattern (16 bp):
GTCCCGAAGAACATAG
Found at i:2763076 original size:22 final size:23
Alignment explanation
Indices: 2763051--2763099 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
2763041 CACATGTATG
*
2763051 TATAAACATCTATCTCATAT-CA
1 TATAAACATCTATCACATATACA
* *
2763073 TAT-AACATGTATCACTTATACA
1 TATAAACATCTATCACATATACA
2763095 TATAA
1 TATAA
2763100 TCACATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 13 0.59
22 8 0.36
23 1 0.05
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.37
Consensus pattern (23 bp):
TATAAACATCTATCACATATACA
Found at i:2763618 original size:3 final size:3
Alignment explanation
Indices: 2763610--2763666 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
2763600 TTCATTTTAA
** * * *
2763610 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT AAT AGT AAT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
2763656 ATT ATTT ATT A
1 ATT A-TT ATT A
2763667 AATATTACAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:2763626 original size:15 final size:15
Alignment explanation
Indices: 2763608--2763637 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2763598 TTTTCATTTT
2763608 AAATTATTATTATTA
1 AAATTATTATTATTA
2763623 AAATTATTATTATTA
1 AAATTATTATTATTA
2763638 TTAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATTATTATTATTA
Found at i:2763636 original size:21 final size:21
Alignment explanation
Indices: 2763610--2763673 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 21
2763600 TTCATTTTAA
2763610 ATTATTATTATTAAAATTATT
1 ATTATTATTATTAAAATTATT
* *
2763631 ATTATTATTAATAGTAA-TATT
1 ATTATTATTATTA-AAATTATT
2763652 ATTTATTATTTATTAAATATTA
1 A-TTATTA-TTATTAAA-ATTA
2763674 CAAAGCCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 17 0.50
22 9 0.26
23 6 0.18
24 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTATTATTATTAAAATTATT
Found at i:2765527 original size:111 final size:111
Alignment explanation
Indices: 2765313--2765527 Score: 281
Period size: 111 Copynumber: 1.9 Consensus size: 111
2765303 ATATCGAATT
* *
2765313 AAAGAGCTGTCTTAAGGCACCTAGAAGCCATTTTCTGATATTTTTGAATAAATAAATATCTTACT
1 AAAGAGCTGTCTTAAGGCACCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
* * * *
2765378 ATATTAAAATAAAATGTTTTTGATATTTATTTTTAAATATCAAAGA
66 ATATTAAAATAAAATATTTTTGAAAATTATTTTGAAATATCAAAGA
* *
2765424 AAAGAGCTGTCTTAAGGTACCTAGAAGCCATTTTCTGATATTTCTAAATAAGTAAATATCTTA-T
1 AAAGAGCTGTCTTAAGGCACCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
* * * * *
2765488 TTATGTATATTAATATATTTTCTTAAAATTA-TTTGAAATA
66 ATAT-TAAAATAAAATATTTT-TGAAAATTATTTTGAAATA
2765528 GTAGAATTAT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
110 4 0.04
111 79 0.89
112 6 0.07
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.41
Consensus pattern (111 bp):
AAAGAGCTGTCTTAAGGCACCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
ATATTAAAATAAAATATTTTTGAAAATTATTTTGAAATATCAAAGA
Found at i:2774802 original size:22 final size:21
Alignment explanation
Indices: 2774776--2774853 Score: 86
Period size: 22 Copynumber: 3.7 Consensus size: 21
2774766 TACATCTACA
2774776 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATT-T
2774798 CTCTTCAAAGATGATAGATTT
1 CTCTTCAAAGATGATAGATTT
* * * *
2774819 -TTTTAAAATATGACAGATTTT
1 CTCTTCAAAGATGATAGA-TTT
*
2774840 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
2774854 AAGCTTTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.27
21 4 0.08
22 31 0.65
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (21 bp):
CTCTTCAAAGATGATAGATTT
Found at i:2775630 original size:76 final size:76
Alignment explanation
Indices: 2775550--2776054 Score: 663
Period size: 76 Copynumber: 6.5 Consensus size: 76
2775540 CTATTTCCCA
* * *
2775550 CATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2775615 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2775626 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2775691 AGCCTTCGGGT
66 AGCCTTCGGGT
* * *
2775702 CATCTGTAAGTCATTCAGTGCATGATG-TTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
* *
2775766 AAACCTTTGGGT
65 AAGCCTTCGGGT
*
2775778 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2775843 AGCCTTCGGGT
66 AGCCTTCGGGT
* ** * ** **
2775854 CATCTGTAAGTCCTTCAGTGCATGATGTTAAAAATGATGTTTCAAAAAAAACCTTCGG-GAGCTT
1 CATCTGTAAGCCCTTCAGTGC---ATG------ATG-T-TTTC-AAAAAGCCTTCGGGAG-CTTT
*
2775918 TTTGATGTTTTCAAAGCCTTAGGGT
53 TT-GATGTTTTCAAAGCCTTCGGGT
* *
2775943 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2776008 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2776019 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
2776055 CCTGCGGGTC
Statistics
Matches: 373, Mismatches: 39, Indels: 34
0.84 0.09 0.08
Matches are distributed among these distances:
75 3 0.01
76 278 0.75
77 16 0.04
78 4 0.01
79 4 0.01
80 3 0.01
85 3 0.01
86 4 0.01
87 4 0.01
88 13 0.03
89 41 0.11
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:2775799 original size:152 final size:153
Alignment explanation
Indices: 2775550--2776054 Score: 798
Period size: 152 Copynumber: 3.2 Consensus size: 153
2775540 CTATTTCCCA
* * *
2775550 CATCTGTAAGTCCTGCAGTGCATGATGTTTTC-AAAAAGCATTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCA
*
2775614 AAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
2775679 TGATGTTTTCAAAGCCTTCGGGT
131 TGATGTTTTCAAAGCCTTCGGGT
*
2775702 CATCTGTAAGTCATTCAGTGCATGATG-TTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCA
* *
2775766 AAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
2775831 TGATGTTTTCAAAGCCTTCGGGT
131 TGATGTTTTCAAAGCCTTCGGGT
2775854 CATCTGTAAGTCCTTCAGTGCATGATGTTAAAAATGATGTTTCAAAAAAAACCTTCGGGAGCTTT
1 CATCTGTAAGTCCTTCAGTGC---ATG------ATG-T-TTTC-AAAAAAACCTTCGGGAGCTTT
2775919 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCT
54 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCT
*
2775984 TCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
119 TCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
* *
2776019 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAA
2776055 CCTGCGGGTC
Statistics
Matches: 327, Mismatches: 12, Indels: 27
0.89 0.03 0.07
Matches are distributed among these distances:
151 4 0.01
152 161 0.49
153 4 0.01
154 4 0.01
155 4 0.01
156 3 0.01
161 3 0.01
162 3 0.01
164 4 0.01
165 137 0.42
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (153 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
TGATGTTTTCAAAGCCTTCGGGT
Found at i:2775949 original size:89 final size:88
Alignment explanation
Indices: 2775799--2775971 Score: 301
Period size: 89 Copynumber: 2.0 Consensus size: 88
2775789 CCTTCAGTGC
* * *
2775799 ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAG
1 ATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAG
*
2775864 TCCTTCAGTGCATGATGTTAAAA
66 CCCTTCAGTGCATGATGTTAAAA
2775887 ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
1 ATGATGTTTC-AAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
2775952 GCCCTTCAGTGCATGATGTT
65 GCCCTTCAGTGCATGATGTT
2775972 TCCAAAAAGC
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
88 10 0.12
89 70 0.88
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (88 bp):
ATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAG
CCCTTCAGTGCATGATGTTAAAA
Found at i:2775994 original size:165 final size:164
Alignment explanation
Indices: 2775723--2776047 Score: 596
Period size: 165 Copynumber: 2.0 Consensus size: 164
2775713 CATTCAGTGC
*
2775723 ATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTTGGGTCATCTGTAAG
1 ATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAG
*
2775788 CCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
66 CCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGG
* *
2775853 TCATCTGTAAGTCCTTCAGTGCATGATGTTAAAA
131 TCATCTATAAGCCCTTCAGTGCATGATGTTAAAA
*
2775887 ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
1 ATGATGTTTC-AAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAA
2775952 GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGG
65 GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGG
2776017 GTCATCTATAAGCCCTTCAGTGCATGATGTT
130 GTCATCTATAAGCCCTTCAGTGCATGATGTT
2776048 TTCAAAACCT
Statistics
Matches: 155, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
164 10 0.06
165 145 0.94
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (164 bp):
ATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAG
CCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGG
TCATCTATAAGCCCTTCAGTGCATGATGTTAAAA
Found at i:2776050 original size:45 final size:45
Alignment explanation
Indices: 2775996--2776109 Score: 165
Period size: 45 Copynumber: 2.5 Consensus size: 45
2775986 GGGAGCTTTT
*
2775996 TGATATTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
* * *
2776041 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
*
2776086 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
2776110 AGCTTTTTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 50 0.83
47 10 0.17
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
Found at i:2776120 original size:197 final size:198
Alignment explanation
Indices: 2775887--2776251 Score: 606
Period size: 197 Copynumber: 1.8 Consensus size: 198
2775877 GATGTTAAAA
2775887 ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
1 ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
* * *
2775952 GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGG
66 GCCCTTCAGTGCATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGG
*
2776017 GTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAG
131 GTCATCTATAAGCCCTTCAGTGCATGATGTTTCCAAAACCTGCGGGTCATCTGTAAGCCCTTCAG
2776082 TGC
196 TGC
* * *
2776085 ATGATGTTTC-CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAA
1 ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
* * * * *
2776149 GTCCTTCAGTGCATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTTAAAATCTTTGG
66 GCCCTTCAGTGCATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGG
*
2776214 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAA
131 GTCATCTATAAGCCCTTCAGTGCATGATGTTTCCAAAA
2776252 AGCCTTTGGG
Statistics
Matches: 154, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
197 144 0.94
198 10 0.06
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (198 bp):
ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
GCCCTTCAGTGCATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGG
GTCATCTATAAGCCCTTCAGTGCATGATGTTTCCAAAACCTGCGGGTCATCTGTAAGCCCTTCAG
TGC
Found at i:2776121 original size:76 final size:76
Alignment explanation
Indices: 2776041--2776294 Score: 402
Period size: 76 Copynumber: 3.3 Consensus size: 76
2776031 CTTCAGTGCA
*
2776041 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2776106 CGGGAGCTTTT
66 CGGGAGCTTTT
* * * *
2776117 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAACCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2776182 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
2776193 TGATGTTTTTAAAATCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
2776258 TGGGAGCTTTT
66 CGGGAGCTTTT
*
2776269 TGATGTTTTC-AAACCCTCAGGGTCAT
1 TGATGTTTTCAAAACCTTC-GGGTCAT
2776295 TCATAAGACC
Statistics
Matches: 160, Mismatches: 17, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
75 5 0.03
76 155 0.97
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:2776134 original size:121 final size:121
Alignment explanation
Indices: 2775920--2776174 Score: 449
Period size: 121 Copynumber: 2.1 Consensus size: 121
2775910 GGGAGCTTTT
* *
2775920 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTGAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2775985 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
*
2776041 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTGAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* * *
2776106 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
2776162 TGATG-TTTCAAAA
1 TGATGTTTTCAAAA
2776175 AAACCTTCGG
Statistics
Matches: 128, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
120 8 0.06
121 120 0.94
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTGAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
Found at i:2776459 original size:3 final size:3
Alignment explanation
Indices: 2776451--2776528 Score: 75
Period size: 3 Copynumber: 25.3 Consensus size: 3
2776441 TTCATTTTAA
** **
2776451 ATT ATT ATT ATT AAA ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
2776499 ATT AAT AGT AAT ATT ATTT ATT ATTT ATT A
1 ATT ATT ATT ATT ATT A-TT ATT A-TT ATT A
2776529 AATATTACAA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:2780198 original size:3 final size:3
Alignment explanation
Indices: 2780190--2780338 Score: 217
Period size: 3 Copynumber: 49.7 Consensus size: 3
2780180 TTTTTATCCA
* * *
2780190 TAT TAT TAT TAT TAA TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2780238 TAT TAT TAA TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2780286 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAC TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2780334 TAT TA
1 TAT TA
2780339 AATATATATT
Statistics
Matches: 128, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 128 1.00
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2782491 original size:6 final size:7
Alignment explanation
Indices: 2782470--2782494 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2782460 TGTCTCTATT
2782470 AATTAAA
1 AATTAAA
2782477 AATTAAA
1 AATTAAA
2782484 AATTAAA
1 AATTAAA
2782491 AATT
1 AATT
2782495 TTTAATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:2793198 original size:9 final size:9
Alignment explanation
Indices: 2793177--2793235 Score: 72
Period size: 9 Copynumber: 6.9 Consensus size: 9
2793167 ATTATGCTTG
2793177 AAGAAAAAGA
1 AAGAAAAA-A
2793187 AAGAAAAAA
1 AAGAAAAAA
2793196 AAGAAAAAA
1 AAGAAAAAA
*
2793205 AAG--AGAA
1 AAGAAAAAA
2793212 AAG-AAAAA
1 AAGAAAAAA
2793220 AAG-AAAAA
1 AAGAAAAAA
2793228 AAGAAAAA
1 AAGAAAAA
2793236 GGGGGTCAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
7 6 0.13
8 14 0.31
9 17 0.38
10 8 0.18
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:2793204 original size:8 final size:8
Alignment explanation
Indices: 2793181--2793235 Score: 67
Period size: 8 Copynumber: 6.6 Consensus size: 8
2793171 TGCTTGAAGA
2793181 AAAAGAAAG
1 AAAA-AAAG
2793190 AAAAAAAAG
1 -AAAAAAAG
2793199 AAAAAAA-
1 AAAAAAAG
*
2793206 AGAGAAAAG
1 A-AAAAAAG
2793215 AAAAAAAG
1 AAAAAAAG
2793223 AAAAAAAG
1 AAAAAAAG
2793231 AAAAA
1 AAAAA
2793236 GGGGGTCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
7 1 0.02
8 31 0.76
9 5 0.12
10 4 0.10
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2793215 original size:16 final size:17
Alignment explanation
Indices: 2793177--2793235 Score: 77
Period size: 16 Copynumber: 3.5 Consensus size: 17
2793167 ATTATGCTTG
2793177 AAGAAAAAGAAAGAAAAAA
1 AAGAAAAA-AAAG-AAAAA
*
2793196 AAGAAAAAAAAG-AGAA
1 AAGAAAAAAAAGAAAAA
2793212 AAG-AAAAAAAGAAAAA
1 AAGAAAAAAAAGAAAAA
2793228 AAGAAAAA
1 AAGAAAAA
2793236 GGGGGTCAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.22
16 12 0.33
17 4 0.11
18 4 0.11
19 8 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAGAAAAA
Found at i:2793573 original size:16 final size:16
Alignment explanation
Indices: 2793547--2793591 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2793537 TTTGAATACA
*
2793547 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
2793564 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
2793579 ATTCAATTTATTT
1 ATTCAATTTATTT
2793592 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:2794501 original size:84 final size:84
Alignment explanation
Indices: 2794360--2794767 Score: 773
Period size: 84 Copynumber: 4.9 Consensus size: 84
2794350 ATATCTTAGT
2794360 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
2794425 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
*
2794444 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
2794509 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
2794528 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
2794593 CTGATCTGGTTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
2794612 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
2794677 CTGATCTGGTTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
*
2794696 TCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
2794760 CTGATCTG
66 CTGATCTG
2794768 GTTTAGTAGG
Statistics
Matches: 320, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
83 42 0.13
84 278 0.87
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAA
Found at i:2795621 original size:113 final size:113
Alignment explanation
Indices: 2795418--2796089 Score: 1150
Period size: 113 Copynumber: 6.0 Consensus size: 113
2795408 CAAAGATTCA
* ** *
2795418 AATCTATCATTTGAAAGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
2795483 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
2795531 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
2795596 AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
2795644 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
2795709 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
2795757 AATCCATCATTTGA-GAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATG-GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
2795821 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
2795870 AATCCATCATTTGAGGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
2795935 AGGAAGAAGAAGTTCATAATTAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * ** * *
2795983 AATTCATCAATTGATGGATTATTTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATATGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
2796047 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
2796090 GCATAATTTT
Statistics
Matches: 538, Mismatches: 19, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
112 70 0.13
113 467 0.87
114 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:2796416 original size:3 final size:3
Alignment explanation
Indices: 2796408--2796553 Score: 229
Period size: 3 Copynumber: 48.7 Consensus size: 3
2796398 TTTTTATCCA
* *
2796408 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
2796456 TAA TAT TAT TGT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2796504 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2796552 TA
1 TA
2796554 AATATATATT
Statistics
Matches: 129, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 129 1.00
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2806111 original size:22 final size:21
Alignment explanation
Indices: 2806085--2806162 Score: 86
Period size: 22 Copynumber: 3.7 Consensus size: 21
2806075 TACATCTACA
2806085 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATT-T
2806107 CTCTTCAAAGATGATAGATTT
1 CTCTTCAAAGATGATAGATTT
* * * *
2806128 -TTTTAAAATATGACAGATTTT
1 CTCTTCAAAGATGATAGA-TTT
*
2806149 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
2806163 AAGCTTTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.27
21 4 0.08
22 31 0.65
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (21 bp):
CTCTTCAAAGATGATAGATTT
Found at i:2809964 original size:22 final size:21
Alignment explanation
Indices: 2809938--2810015 Score: 86
Period size: 22 Copynumber: 3.7 Consensus size: 21
2809928 TACATCTACA
2809938 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATT-T
2809960 CTCTTCAAAGATGATAGATTT
1 CTCTTCAAAGATGATAGATTT
* * * *
2809981 -TTTTAAAATATGACAGATTTT
1 CTCTTCAAAGATGATAGA-TTT
*
2810002 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
2810016 AAGCTTTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.27
21 4 0.08
22 31 0.65
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (21 bp):
CTCTTCAAAGATGATAGATTT
Found at i:2810810 original size:45 final size:45
Alignment explanation
Indices: 2810761--2810874 Score: 192
Period size: 45 Copynumber: 2.5 Consensus size: 45
2810751 GGGAGCTTTT
2810761 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
2810806 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
2810851 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
2810875 AGCTTTTTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 53 0.83
47 11 0.17
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:2810886 original size:76 final size:76
Alignment explanation
Indices: 2810806--2811333 Score: 734
Period size: 76 Copynumber: 6.8 Consensus size: 76
2810796 CTTCAGTGCA
*
2810806 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2810871 CGGGAGCTTTT
66 CGGGAGCTTTT
*
2810882 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2810947 CGGGAGCTTTT
66 CGGGAGCTTTT
** * *
2810958 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAATCCTTCAGTGCATGATGTTTCAAAAAAACCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
2811023 CAGGAGCTTTT
66 CGGGAGCTTTT
* *
2811034 TGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2811099 CGGGAGCTTTT
66 CGGGAGCTTTT
*
2811110 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTAAAAATGATGTTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGC------------ATGATGTTT
* ** * ** **
2811175 CAAAAAAAACCTTCGG-GAGCTTT
54 CCAAAAAGCCTTCGGGAG-CTTTT
*
2811198 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCT
1 T-GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCT
2811263 TCGGGAGCTTTT
65 TCGGGAGCTTTT
* *
2811275 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAA
2811334 CCTGCGGGTC
Statistics
Matches: 400, Mismatches: 37, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
76 311 0.78
77 23 0.06
78 1 0.00
87 1 0.00
88 23 0.06
89 41 0.10
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:2810922 original size:121 final size:123
Alignment explanation
Indices: 2810708--2810950 Score: 420
Period size: 121 Copynumber: 2.0 Consensus size: 123
2810698 CTATTTCCCA
* *
2810708 CATCTGTAAGTCCTGTAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2810773 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGT
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGT
2810829 CATCTGTAAGCCCT-TCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTGT-AGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
2810893 AAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
65 AAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
2810951 AGCTTTTTGA
Statistics
Matches: 115, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
120 1 0.01
121 102 0.89
122 4 0.03
123 8 0.07
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (123 bp):
CATCTGTAAGCCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGT
Found at i:2811006 original size:152 final size:152
Alignment explanation
Indices: 2810806--2811333 Score: 822
Period size: 152 Copynumber: 3.4 Consensus size: 152
2810796 CTTCAGTGCA
* * *
2810806 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCAAAAAAACCTT
* *
2810871 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
2810936 CAAAAAGCCTTCGGGAGCTTTT
131 CAAAAAGCCTTCGGGAGCTTTT
**
2810958 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAATCCTTCAGTGCATGATGTTTCAAAAAAACCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCAAAAAAACCTT
* * *
2811023 CAGGAGCTTTTTGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
2811088 CAAAAAGCCTTCGGGAGCTTTT
131 CAAAAAGCCTTCGGGAGCTTTT
*
2811110 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTAAAAATGATGTTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGC------------ATGATGTTT
2811175 CAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAG
54 C-AAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAG
2811240 TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
118 TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
2811275 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTTCAAAA
2811334 CCTGCGGGTC
Statistics
Matches: 347, Mismatches: 15, Indels: 27
0.89 0.04 0.07
Matches are distributed among these distances:
152 186 0.54
153 10 0.03
154 4 0.01
164 10 0.03
165 137 0.39
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (152 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCAAAAAAACCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
CAAAAAGCCTTCGGGAGCTTTT
Found at i:2811228 original size:89 final size:88
Alignment explanation
Indices: 2811078--2811250 Score: 301
Period size: 89 Copynumber: 2.0 Consensus size: 88
2811068 CCTTCAGTGC
* * *
2811078 ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAG
1 ATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAG
*
2811143 TCCTTCAGTGCATGATGTTAAAA
66 CCCTTCAGTGCATGATGTTAAAA
2811166 ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
1 ATGATGTTTC-AAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
2811231 GCCCTTCAGTGCATGATGTT
65 GCCCTTCAGTGCATGATGTT
2811251 TCCAAAAAGC
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
88 10 0.12
89 70 0.88
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (88 bp):
ATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAG
CCCTTCAGTGCATGATGTTAAAA
Found at i:2811273 original size:165 final size:164
Alignment explanation
Indices: 2811002--2811326 Score: 596
Period size: 165 Copynumber: 2.0 Consensus size: 164
2810992 CCTTCAGTGC
*
2811002 ATGATGTTTCAAAAAAACCTTCAGGAGCTTTTTGATGTTTTCAAAACCTTTGGGTCATCTGTAAG
1 ATGATGTTTCAAAAAAACCTTCAGGAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAG
2811067 CCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
66 CCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
* *
2811132 TCATCTGTAAGTCCTTCAGTGCATGATGTTAAAA
131 TCATCTATAAGCCCTTCAGTGCATGATGTTAAAA
* *
2811166 ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
1 ATGATGTTTC-AAAAAAACCTTCAGGAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAA
2811231 GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGG
65 GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGG
2811296 GTCATCTATAAGCCCTTCAGTGCATGATGTT
130 GTCATCTATAAGCCCTTCAGTGCATGATGTT
2811327 TTCAAAACCT
Statistics
Matches: 155, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
164 10 0.06
165 145 0.94
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (164 bp):
ATGATGTTTCAAAAAAACCTTCAGGAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAG
CCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
TCATCTATAAGCCCTTCAGTGCATGATGTTAAAA
Found at i:2811324 original size:45 final size:45
Alignment explanation
Indices: 2811275--2811388 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
2811265 GGGAGCTTTT
2811275 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
* * *
2811320 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
*
2811365 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
2811389 AGCTTTTTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 51 0.84
47 10 0.16
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
Found at i:2811391 original size:197 final size:198
Alignment explanation
Indices: 2811166--2811530 Score: 633
Period size: 197 Copynumber: 1.8 Consensus size: 198
2811156 GATGTTAAAA
2811166 ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
1 ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
* * *
2811231 GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGG
66 GCCCTTCAGTGCATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGG
*
2811296 GTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAG
131 GTCATCTATAAGCCCTTCAGTGCATGATGTTTCCAAAACCTGCGGGTCATCTGTAAGCCCTTCAG
2811361 TGC
196 TGC
* * *
2811364 ATGATGTTTC-CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAA
1 ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
* *
2811428 GTCCTTCAGTGCATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTTGG
66 GCCCTTCAGTGCATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGG
*
2811493 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAA
131 GTCATCTATAAGCCCTTCAGTGCATGATGTTTCCAAAA
2811531 AGCCTTTGGA
Statistics
Matches: 157, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
197 147 0.94
198 10 0.06
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (198 bp):
ATGATGTTTCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
GCCCTTCAGTGCATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGG
GTCATCTATAAGCCCTTCAGTGCATGATGTTTCCAAAACCTGCGGGTCATCTGTAAGCCCTTCAG
TGC
Found at i:2811400 original size:76 final size:76
Alignment explanation
Indices: 2811320--2811573 Score: 411
Period size: 76 Copynumber: 3.3 Consensus size: 76
2811310 CTTCAGTGCA
*
2811320 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2811385 CGGGAGCTTTT
66 CGGGAGCTTTT
* * * *
2811396 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAACCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2811461 CGGGAGCTTTT
66 CGGGAGCTTTT
*
2811472 TGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* *
2811537 TGGAAGCTTTT
66 CGGGAGCTTTT
*
2811548 TGATGTTTTC-AAACCCTCAGGGTCAT
1 TGATGTTTTCAAAACCTTC-GGGTCAT
2811574 TCATAAGACC
Statistics
Matches: 163, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
75 6 0.04
76 157 0.96
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:2811413 original size:121 final size:121
Alignment explanation
Indices: 2811199--2811453 Score: 458
Period size: 121 Copynumber: 2.1 Consensus size: 121
2811189 GGGAGCTTTT
* *
2811199 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTGAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2811264 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
*
2811320 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTGAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* *
2811385 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
2811441 TGATG-TTTCAAAA
1 TGATGTTTTCAAAA
2811454 AAACCTTCGG
Statistics
Matches: 129, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
120 8 0.06
121 121 0.94
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTGAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCA
Found at i:2811738 original size:3 final size:3
Alignment explanation
Indices: 2811730--2811800 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
2811720 TTCATTTTAA
** **
2811730 ATT ATT ATT ATT AAA ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
2811778 AAT A-T ATT ATTT ATT ATTT ATT A
1 ATT ATT ATT A-TT ATT A-TT ATT A
2811801 AATATTACAA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.04
3 48 0.86
4 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:2811791 original size:21 final size:19
Alignment explanation
Indices: 2811730--2811807 Score: 88
Period size: 18 Copynumber: 4.1 Consensus size: 19
2811720 TTCATTTTAA
2811730 ATTATTATTATTAAA-ATT
1 ATTATTATTATTAAATATT
** *
2811748 AAAATTATTATT-ATTATT
1 ATTATTATTATTAAATATT
2811766 ATTATTATTATTAATATATT
1 ATTATTATTATTAA-ATATT
2811786 ATTTATTATTTATTAAATATT
1 A-TTATTA-TTATTAAATATT
2811807 A
1 A
2811808 CAAAGCCCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
17 1 0.02
18 23 0.47
19 1 0.02
20 5 0.10
21 12 0.24
22 7 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATTATTATTAAATATT
Found at i:2813643 original size:111 final size:111
Alignment explanation
Indices: 2813429--2813643 Score: 263
Period size: 111 Copynumber: 1.9 Consensus size: 111
2813419 ATATCGAATT
* *
2813429 AAAGAGCTGTCTTAAGGCACATAGAAGCCATTTTCTGATATTTTTGAATAAATAAATATCTTACT
1 AAAGAGCTGTCTTAAGGCACATAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
* * * *
2813494 ATATTAAAATAAAATGTTTTTGATATTTATTTTTAAATATCAAAGA
66 ATATTAAAATAAAATATTTTTGAAAATTATTTTGAAATATCAAAGA
* * * *
2813540 AAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTCTAAATAAGTAAATATCTTA-T
1 AAAGAGCTGTCTTAAGGCACATAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
* * * * *
2813604 TTATGTATATTAATATATTTTCTTAAAATTA-TTTGAAATA
66 ATAT-TAAAATAAAATATTTT-TGAAAATTATTTTGAAATA
2813644 GTAGAATTAT
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
110 4 0.05
111 77 0.89
112 6 0.07
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.41
Consensus pattern (111 bp):
AAAGAGCTGTCTTAAGGCACATAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
ATATTAAAATAAAATATTTTTGAAAATTATTTTGAAATATCAAAGA
Found at i:2815159 original size:14 final size:14
Alignment explanation
Indices: 2815140--2815172 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2815130 CACGGGGAAA
*
2815140 AAGAAAGCAAGAAG
1 AAGAAAGCAAAAAG
2815154 AAGAAAGCAAAAAG
1 AAGAAAGCAAAAAG
2815168 AAGAA
1 AAGAA
2815173 GAAAGTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.06, G:0.24, T:0.00
Consensus pattern (14 bp):
AAGAAAGCAAAAAG
Found at i:2818162 original size:31 final size:31
Alignment explanation
Indices: 2818124--2818184 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
2818114 CCCGAAGGAC
*
2818124 CAGTCCATATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
2818155 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
2818185 CCCTCGACTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:2818260 original size:22 final size:21
Alignment explanation
Indices: 2818229--2818280 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
2818219 CTCTTATATC
*
2818229 ATATAACATGGGCATTCTCTT
1 ATATCACATGGGCATTCTCTT
**
2818250 ATAATCACATGTTCATTCTCTT
1 AT-ATCACATGGGCATTCTCTT
*
2818272 CTATCACAT
1 ATATCACAT
2818281 ACCACATGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (21 bp):
ATATCACATGGGCATTCTCTT
Found at i:2818321 original size:21 final size:22
Alignment explanation
Indices: 2818297--2818337 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2818287 TGTATGTATA
* *
2818297 AACATTTATCTCATA-ACATAT
1 AACATGTATCACATATACATAT
2818318 AACATGTATCACATATACAT
1 AACATGTATCACATATACAT
2818338 GTAATCACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (22 bp):
AACATGTATCACATATACATAT
Found at i:2818333 original size:16 final size:17
Alignment explanation
Indices: 2818312--2818356 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
2818302 TTATCTCATA
2818312 ACATATAACATGT-ATC
1 ACATATAACATGTAATC
2818328 ACATAT-ACATGTAATC
1 ACATATAACATGTAATC
*
2818344 ACATATATCATGT
1 ACATATAACATGT
2818357 CTCGTAGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.23
16 15 0.58
17 5 0.19
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (17 bp):
ACATATAACATGTAATC
Found at i:2819997 original size:14 final size:14
Alignment explanation
Indices: 2819977--2820010 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2819967 AGCATACGGG
2819977 GAAGAAGAAAGCAA
1 GAAGAAGAAAGCAA
*
2819991 TAAGAAGAAAGCAA
1 GAAGAAGAAAGCAA
2820005 GAAGAA
1 GAAGAA
2820011 TAATAGAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.26, T:0.03
Consensus pattern (14 bp):
GAAGAAGAAAGCAA
Found at i:2827508 original size:15 final size:15
Alignment explanation
Indices: 2827488--2827518 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2827478 ACAATAAAAT
2827488 TATATTATATTAGAA
1 TATATTATATTAGAA
2827503 TATATTATATTAGAA
1 TATATTATATTAGAA
2827518 T
1 T
2827519 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TATATTATATTAGAA
Found at i:2827757 original size:2 final size:2
Alignment explanation
Indices: 2827750--2827873 Score: 61
Period size: 2 Copynumber: 67.0 Consensus size: 2
2827740 TAAAAATAAT
* *
2827750 TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
2827789 -A TT TA AA T- TA -A AA AA TA TA TA TA -A TA TT 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
* * * * * *
2827827 -A TT TA AA TA TA TA TA TA -A TA TT TA TA TA TT TA -A TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2827866 TA TA TA TA
1 TA TA TA TA
2827874 CCCGGCCCAA
Statistics
Matches: 89, Mismatches: 23, Indels: 20
0.67 0.17 0.15
Matches are distributed among these distances:
1 10 0.11
2 79 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2827807 original size:38 final size:33
Alignment explanation
Indices: 2827764--2827873 Score: 134
Period size: 32 Copynumber: 3.2 Consensus size: 33
2827754 TATATATATA
* *
2827764 TATATATATAATATTAATAAATTTAATTTAAAT
1 TATATATATAATATTTATATATTTAATTTAAAT
*
2827797 TAAAAAATATATATAATATTTATATATATAATTTAAA-
1 T-----ATATATATAATATTTATATATTTAATTTAAAT
2827834 TATATATATAATATTTATATATTTAATTTAAA-
1 TATATATATAATATTTATATATTTAATTTAAAT
2827866 TATATATA
1 TATATATA
2827874 CCCGGCCCAA
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
32 38 0.56
33 1 0.01
37 1 0.01
38 28 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
TATATATATAATATTTATATATTTAATTTAAAT
Found at i:2827823 original size:15 final size:15
Alignment explanation
Indices: 2827803--2827873 Score: 74
Period size: 15 Copynumber: 4.6 Consensus size: 15
2827793 AAATTAAAAA
2827803 ATATATATAATATT-T
1 ATATATATAAT-TTAT
2827818 ATATATATAATTTAAAT
1 ATATATATAATTT--AT
2827835 ATATATATAATATT-T
1 ATATATATAAT-TTAT
* *
2827850 ATATATTTAATTTAA
1 ATATATATAATTTAT
2827865 ATATATATA
1 ATATATATA
2827874 CCCGGCCCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
14 4 0.08
15 30 0.62
17 12 0.25
18 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATATAATTTAT
Found at i:2827825 original size:17 final size:17
Alignment explanation
Indices: 2827803--2827855 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
2827793 AAATTAAAAA
2827803 ATATATATAATA-TT-T
1 ATATATATAATATTTAT
*
2827818 ATATATATAAT-TTAAAT
1 ATATATATAATATT-TAT
2827835 ATATATATAATATTTAT
1 ATATATATAATATTTAT
2827852 ATAT
1 ATAT
2827856 TTAATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 12 0.38
17 18 0.56
18 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATATAATATTTAT
Found at i:2827869 original size:17 final size:17
Alignment explanation
Indices: 2827817--2827873 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
2827807 ATATAATATT
2827817 TATATATATAATTTAAA
1 TATATATATAATTTAAA
2827834 TATATATATAATATT---
1 TATATATATAAT-TTAAA
*
2827849 TATATATTTAATTTAAA
1 TATATATATAATTTAAA
2827866 TATATATA
1 TATATATA
2827874 CCCGGCCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
17 19 0.56
18 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATATATAATTTAAA
Found at i:2834263 original size:33 final size:33
Alignment explanation
Indices: 2834198--2834290 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
2834188 GCTGGGCATC
* * * * * *
2834198 CGAGAGCAACCGAGGTCATCCGAACGAGCTATG
1 CGAGGGCATCCGAGGGCAACCGAGCGAACTATG
2834231 CGAGGGCATCCGAGGGCAACCGAGCGAACTATG
1 CGAGGGCATCCGAGGGCAACCGAGCGAACTATG
*
2834264 CGAGGGAATCCGAGGGCAACCGAGCGA
1 CGAGGGCATCCGAGGGCAACCGAGCGA
2834291 GGGTAGGTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.29, C:0.27, G:0.35, T:0.09
Consensus pattern (33 bp):
CGAGGGCATCCGAGGGCAACCGAGCGAACTATG
Found at i:2834395 original size:23 final size:23
Alignment explanation
Indices: 2834344--2834392 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2834334 TGCTCAGATT
* *
2834344 CCCTCGCATAGTTCGCTCGGTTG
1 CCCTCGCATAGCTCGCTCGGTAG
*
2834367 CCCTCGCATAGCTCGTTCGGATAG
1 CCCTCGCATAGCTCGCTCGG-TAG
2834391 CC
1 CC
2834393 TCGGTTGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.12, C:0.37, G:0.24, T:0.27
Consensus pattern (23 bp):
CCCTCGCATAGCTCGCTCGGTAG
Found at i:2834407 original size:20 final size:20
Alignment explanation
Indices: 2834382--2834437 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
2834372 GCATAGCTCG
*
2834382 TTCGGATAGCCTCGGTTGCT
1 TTCGGATGGCCTCGGTTGCT
*
2834402 TTCGGATGGCCTCGGATGCT
1 TTCGGATGGCCTCGGTTGCT
2834422 TTCGGATGGCCTCGGT
1 TTCGGATGGCCTCGGT
2834438 CGAATGGCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.09, C:0.25, G:0.34, T:0.32
Consensus pattern (20 bp):
TTCGGATGGCCTCGGTTGCT
Found at i:2834535 original size:30 final size:30
Alignment explanation
Indices: 2834501--2834632 Score: 196
Period size: 29 Copynumber: 4.5 Consensus size: 30
2834491 CTGCATGGAT
*
2834501 TGCATGGCGACCTACCTAGGTAGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
2834531 TGCATGGCGACCTACCTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
** *
2834561 TGCATGGCGACCT-GGTTGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
**
2834590 TGCATGGCGACCT-GGTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
2834619 TGCATGGCGACCTA
1 TGCATGGCGACCTA
2834633 GATGGGGACT
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 54 0.56
30 42 0.44
ACGTcount: A:0.13, C:0.27, G:0.39, T:0.21
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAGGTCGCTGGGCG
Found at i:2835733 original size:31 final size:33
Alignment explanation
Indices: 2835685--2835760 Score: 79
Period size: 35 Copynumber: 2.3 Consensus size: 33
2835675 GTTTTGGCTT
* *
2835685 ATTGGTTTTGATGATT-A-ATGTTCGGATTGAA
1 ATTGGTTTTTATGATTAACATGTTCAGATTGAA
2835716 ATTGGTTTTTACT-ATTAACTGATGTTCAGATTGAA
1 ATTGGTTTTTA-TGATTAAC--ATGTTCAGATTGAA
2835751 ATT-GTTTTTA
1 ATTGGTTTTTA
2835761 ACTGTATTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 13 0.34
32 2 0.05
34 7 0.18
35 16 0.42
ACGTcount: A:0.26, C:0.05, G:0.20, T:0.49
Consensus pattern (33 bp):
ATTGGTTTTTATGATTAACATGTTCAGATTGAA
Found at i:2847643 original size:22 final size:20
Alignment explanation
Indices: 2847611--2847650 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
2847601 AAAATTAATA
*
2847611 TATTTTATTAAATTAATTCT
1 TATTTTATTAAAATAATTCT
2847631 TATTTTAATTTAAAATAATT
1 TATTTT-A-TTAAAATAATT
2847651 AAATAATCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTATTAAAATAATTCT
Found at i:2849600 original size:18 final size:18
Alignment explanation
Indices: 2849558--2849605 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
2849548 TATATATTAG
2849558 ATATTTGAATTTCATTTTA
1 ATATTT-AATTTCATTTTA
*
2849577 ATATTTAATTTGATATTTA
1 ATATTTAATTTCAT-TTTA
*
2849596 A-ATTTTATTT
1 ATATTTAATTT
2849606 TCTAATTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
ATATTTAATTTCATTTTA
Found at i:2849631 original size:26 final size:25
Alignment explanation
Indices: 2849573--2849631 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
2849563 TGAATTTCAT
* * *
2849573 TTTAATATTTAATTTGATATTTAAA
1 TTTAATTTTTAATTAGATATTCAAA
*
2849598 TTTTATTTTCTAATTAGATATTCAAA
1 TTTAATTTT-TAATTAGATATTCAAA
2849624 TTTAATTT
1 TTTAATTT
2849632 GATATTGACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTAATTTTTAATTAGATATTCAAA
Found at i:2856387 original size:13 final size:14
Alignment explanation
Indices: 2856361--2856389 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2856351 GCAGATCAAG
2856361 AACAATATATAATC
1 AACAATATATAATC
2856375 AACAATA-ATAATC
1 AACAATATATAATC
2856388 AA
1 AA
2856390 ATTAATAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (14 bp):
AACAATATATAATC
Found at i:2856882 original size:16 final size:16
Alignment explanation
Indices: 2856861--2856913 Score: 106
Period size: 16 Copynumber: 3.3 Consensus size: 16
2856851 ACAAAACTTA
2856861 TGAATCATTCAACATT
1 TGAATCATTCAACATT
2856877 TGAATCATTCAACATT
1 TGAATCATTCAACATT
2856893 TGAATCATTCAACATT
1 TGAATCATTCAACATT
2856909 TGAAT
1 TGAAT
2856914 TATTTAACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:2867499 original size:42 final size:42
Alignment explanation
Indices: 2867452--2867577 Score: 119
Period size: 42 Copynumber: 3.2 Consensus size: 42
2867442 CAATGAATGA
2867452 ATGTTTAAAAGGTATATTTATGTTATATATTGATATTTTCAT
1 ATGTTTAAAAGGTATATTTATGTTATATATTGATATTTTCAT
* * * *
2867494 ATGTTT-AAA--TATA-TCAT-TTTTATCAATGA-A---TGA-
1 ATGTTTAAAAGGTATATTTATGTTATAT-ATTGATATTTTCAT
* *
2867527 ACGTTTAAAAGGTACATTTATGTTATATATTGATATTTTCAT
1 ATGTTTAAAAGGTATATTTATGTTATATATTGATATTTTCAT
2867569 ATGTTTAAA
1 ATGTTTAAA
2867578 TATATCTTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 22
0.65 0.12 0.23
Matches are distributed among these distances:
33 5 0.08
34 5 0.08
36 3 0.05
37 13 0.21
38 13 0.21
39 4 0.06
41 5 0.08
42 14 0.23
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (42 bp):
ATGTTTAAAAGGTATATTTATGTTATATATTGATATTTTCAT
Found at i:2867564 original size:75 final size:74
Alignment explanation
Indices: 2867441--2867599 Score: 282
Period size: 75 Copynumber: 2.1 Consensus size: 74
2867431 CTTAAATCAT
* *
2867441 TCAATGAATGAATGTTTAAAAGGTATATTTATGTTATATATTGATATTTTCATATGTTTAAATAT
1 TCAATGAATGAACGTTTAAAAGGTACATTTATGTTATATATTGATATTTTCATATGTTTAAATAT
2867506 ATCATTTTTA
66 ATC-TTTTTA
2867516 TCAATGAATGAACGTTTAAAAGGTACATTTATGTTATATATTGATATTTTCATATGTTTAAATAT
1 TCAATGAATGAACGTTTAAAAGGTACATTTATGTTATATATTGATATTTTCATATGTTTAAATAT
2867581 ATCTTTTTA
66 ATCTTTTTA
*
2867590 TCAATTAATG
1 TCAATGAATG
2867600 TTTAAATATT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 15 0.19
75 66 0.81
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.48
Consensus pattern (74 bp):
TCAATGAATGAACGTTTAAAAGGTACATTTATGTTATATATTGATATTTTCATATGTTTAAATAT
ATCTTTTTA
Found at i:2869235 original size:18 final size:17
Alignment explanation
Indices: 2869212--2869274 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
2869202 GTTTATGAGA
* *
2869212 GAATTGGAATCTGTGAAT
1 GAATTGGAATCTGT-CAG
*
2869230 GAATTGAAATCTGTCAG
1 GAATTGGAATCTGTCAG
*
2869247 GAATTAGAATCTGTCAG
1 GAATTGGAATCTGTCAG
2869264 GAATTGGAATC
1 GAATTGGAATC
2869275 CAATTTTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 26 0.67
18 13 0.33
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (17 bp):
GAATTGGAATCTGTCAG
Found at i:2869841 original size:27 final size:27
Alignment explanation
Indices: 2869801--2869865 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
2869791 CCCGAACCCG
*
2869801 ACCCGACCCGAATATCACACTTAAAAA
1 ACCCGACCCGAATATCAAACTTAAAAA
*
2869828 ATCCGACCCGAATATCAAACTTAAAAA
1 ACCCGACCCGAATATCAAACTTAAAAA
*
2869855 ACCCAACCCGA
1 ACCCGACCCGA
2869866 CCCGAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.45, C:0.34, G:0.08, T:0.14
Consensus pattern (27 bp):
ACCCGACCCGAATATCAAACTTAAAAA
Found at i:2869866 original size:32 final size:30
Alignment explanation
Indices: 2869795--2869871 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 30
2869785 CCTAAACCCG
* *
2869795 AACCCGACCCGACCCGAATATCACACTTAA
1 AACCCAACCCGACCCGAATATCAAACTTAA
*
2869825 AA---AATCCGACCCGAATATCAAACTTAAAA
1 AACCCAACCCGACCCGAATATCAAACTT--AA
2869854 AACCCAACCCGACCCGAA
1 AACCCAACCCGACCCGAA
2869872 CAAAATAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 20 0.53
29 4 0.11
30 2 0.05
32 12 0.32
ACGTcount: A:0.43, C:0.36, G:0.09, T:0.12
Consensus pattern (30 bp):
AACCCAACCCGACCCGAATATCAAACTTAA
Found at i:2876625 original size:36 final size:35
Alignment explanation
Indices: 2876575--2876660 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 35
2876565 TCAAAGTTTA
* * *
2876575 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAAT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGAC-AAAAT
2876611 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
*
2876646 TAATTTCAAGGGAAA
1 T-GTTTCAAGGGAAA
2876661 TGTTTTCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 6 0.13
36 39 0.87
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
Found at i:2876718 original size:65 final size:65
Alignment explanation
Indices: 2876611--2876831 Score: 287
Period size: 65 Copynumber: 3.5 Consensus size: 65
2876601 AGACAAAAAT
*
2876611 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGGAAATGTTTTCAATGTTTA
* * ** * **
2876676 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG--A-G---ACAA-AATT-
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGGAAATGTTTTCAATGTTTA
* *
2876733 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGGAAATGTTTTCAATGTTTA
*
2876798 TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
2876832 CTTAGTTCCA
Statistics
Matches: 130, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
57 42 0.32
58 2 0.02
59 4 0.03
60 1 0.01
62 1 0.01
63 4 0.03
64 2 0.02
65 74 0.57
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:2876721 original size:21 final size:21
Alignment explanation
Indices: 2876695--2876744 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2876685 AGAAACTGTC
2876695 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
2876716 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
2876737 TCAAGGGA
1 TCAAGGGA
2876745 AACTATCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:2876745 original size:122 final size:122
Alignment explanation
Indices: 2876594--2876831 Score: 431
Period size: 122 Copynumber: 2.0 Consensus size: 122
2876584 AGAAACTGTC
2876594 TCAAGGGAGACAAAAATTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGGA
1 TCAAGGGAGACAAAAATTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGGA
* * *
2876659 AATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
66 AATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAATTTGTT
* *
2876716 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGA
1 TCAAGGGAGACAAAAATTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGGA
2876781 AATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAA
66 AATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAA
2876832 CTTAGTTCCA
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 111 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (122 bp):
TCAAGGGAGACAAAAATTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGGA
AATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAATTTGTT
Found at i:2876868 original size:102 final size:102
Alignment explanation
Indices: 2876750--2876933 Score: 289
Period size: 102 Copynumber: 1.8 Consensus size: 102
2876740 AGGGAAACTA
** * *
2876750 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAGAAACT
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGATTT-TGTTTCAAGAGAAACT
2876814 ATCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAAATG
65 ATCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAAATG
**
2876852 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATATTCAAAGATTTTGTTTCAAGAGAAACTA
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGATTTTGTTTCAAGAGAAACTA
*
2876917 TCTTAAGAGAGAAAAAA
66 TCTCAAGAGAGAAAAAA
2876934 TTCATTTCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
102 71 0.96
103 3 0.04
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (102 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGATTTTGTTTCAAGAGAAACTA
TCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAAATG
Found at i:2876937 original size:167 final size:166
Alignment explanation
Indices: 2876685--2877095 Score: 532
Period size: 167 Copynumber: 2.5 Consensus size: 166
2876675 ATGTTTCAAG
* * *
2876685 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG---AGA--CAAA-A-TTTGTTTCAAGG
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAATATTCAAAGATTTTGTTTCAAGA
*
2876743 GAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
66 GAAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
2876808 GAAACTATCTCAAGAGAGAAAAAACTTAGTTCCAAA
131 GAAACTATCTCAAGAGAGAAAAAACTTAGTTCCAAA
*
2876844 AGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA-ATATTCAAAGATTTTGTTTCAAG
* *
2876909 AGAAACTATCTTAAGAGAGAAAAAATTCATTTCAAGTGAAATGTTTTCAATGTTTATGTTTCAAG
65 AGAAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
* * * * * * *
2876974 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAG
130 AGAAACTATCTCAAGAGAGAAAAAACTTAGTTCCAAA
* * * * ** * *
2877011 GGAACCTATCTTAAGAGAGACAAAATTCATTTCAAGGGAAAATTTTTCAATG-TTTATGTTTCAA
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAA-TATTCAAAGATTT-TGTTTCAA
*
2877075 GAGAAACTGTCTCAAGAGAGA
64 GAGAAACTATCTCAAGAGAGA
2877096 CGAAACCTAT
Statistics
Matches: 217, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
159 36 0.17
163 2 0.01
165 4 0.02
166 5 0.02
167 170 0.78
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (166 bp):
AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAATATTCAAAGATTTTGTTTCAAGA
GAAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
GAAACTATCTCAAGAGAGAAAAAACTTAGTTCCAAA
Found at i:2876958 original size:65 final size:65
Alignment explanation
Indices: 2876852--2877014 Score: 184
Period size: 65 Copynumber: 2.5 Consensus size: 65
2876842 AAAGAAAATG
**
2876852 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATATTCAAAGATTT-TGTTTCAAGAGAAACT
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAG-TTTATGTTTCAAGAGAAACT
2876916 A
65 A
* * * ** * * *
2876917 TCTTAAGAGAGAAAAAATTCATTTCAAGTGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTG
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGTTTATGTTTCAAGAGAAACTA
* **
2876982 TCTCAAGGGAGACAAAATTTTGTTTCAAGGGAA
1 TCTCAAGAGAGACAAAA-TTCATTTCAAGGGAA
2877015 CCTATCTTAA
Statistics
Matches: 80, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
64 3 0.04
65 65 0.81
66 12 0.15
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (65 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGTTTATGTTTCAAGAGAAACTA
Found at i:2877002 original size:102 final size:103
Alignment explanation
Indices: 2876891--2877096 Score: 344
Period size: 102 Copynumber: 2.0 Consensus size: 103
2876881 GAAACATATT
*
2876891 CAAAGATTTTGTTTCAAGAGAAACTATCTTAAGAGAGAAAAAATTCATTTCAAGTG-AAATGTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTTAAGAGAGAAAAAATTCATTTCAAGGGAAAAT-TTT
*
2876955 TCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
65 TCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
* * *
2876994 CAAA-ATTTTGTTTCAAGGGAACCTATCTTAAGAGAGACAAAATTCATTTCAAGGGAAAATTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTTAAGAGAGAAAAAATTCATTTCAAGGGAAAATTTTT
2877058 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
66 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
2877096 C
1 C
2877097 GAAACCTATT
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
102 89 0.92
103 8 0.08
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (103 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTTAAGAGAGAAAAAATTCATTTCAAGGGAAAATTTTT
CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
Found at i:2877031 original size:37 final size:36
Alignment explanation
Indices: 2876965--2877051 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 36
2876955 TCAATGTTTA
* * *
2876965 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
* *
2877002 TGTTTCAAGGGAACCTATCTTAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
**
2877038 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
2877052 ATTTTTCAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 13 0.31
37 29 0.69
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:2877133 original size:102 final size:102
Alignment explanation
Indices: 2876902--2877148 Score: 282
Period size: 102 Copynumber: 2.4 Consensus size: 102
2876892 AAAGATTTTG
* * * * *
2876902 TTTCAAGAGAAACTATCTTAAGAGAGAAAAAATTCATTTCAAGTGAAATGTTTTCAATGTTTATG
1 TTTCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
* ** *
2876967 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
66 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATCCTA
** ** *
2877004 TTTCAAGGGAACCTATCTTAAGAGAGACAAAATTCATTTCAAGGGAAAAT-TTTTCAATGTTTAT
1 TTTCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGG-AAATGTTTTCAATGTTTAT
*
2877068 GTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-CCTA
65 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATCCTA
* * * **
2877105 TTTCTAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAG
1 TTTC-AAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAG
2877149 AGAGACAAAA
Statistics
Matches: 124, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
101 5 0.04
102 115 0.93
103 4 0.03
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (102 bp):
TTTCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATCCTA
Found at i:2877294 original size:72 final size:75
Alignment explanation
Indices: 2877177--2877319 Score: 238
Period size: 72 Copynumber: 1.9 Consensus size: 75
2877167 AAAAAATAGT
* *
2877177 CTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGTGAGACAAAGTCTGTTTTA
1 CTTGAGTGAAATGAAAT-CCTTCTTTCGAGTGAAAACAGTCTCAAGTGAGACAAAGTATGTTTTA
2877242 AGAAAAGCAAA
65 AGAAAAGCAAA
2877253 CTTGAGTGAAAT-AAAT-CTTCTTTCGAGT-AAAACAGTCTCAAGTGAGACAAAGTATGTTTTAA
1 CTTGAGTGAAATGAAATCCTTCTTTCGAGTGAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAA
2877315 GAAAA
66 GAAAA
2877320 ACAATCTCAA
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
72 37 0.57
73 12 0.18
75 4 0.06
76 12 0.18
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (75 bp):
CTTGAGTGAAATGAAATCCTTCTTTCGAGTGAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAA
GAAAAGCAAA
Found at i:2877321 original size:36 final size:36
Alignment explanation
Indices: 2877216--2877335 Score: 118
Period size: 36 Copynumber: 3.3 Consensus size: 36
2877206 GTGAAAACGG
*
2877216 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAGCAA
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAA
* ** * * * * *
2877252 ACTTGAGTGAAATAAA-TCT-TCTTTCGAGTAAAACAG
1 TCTCAAGTGAGACAAAGTCTGT-TTT-AAGAAAAACAA
*
2877288 TCTCAAGTGAGACAAAGTATGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAA
2877324 TCTCAAGTGAGA
1 TCTCAAGTGAGA
2877336 TAATCATCTG
Statistics
Matches: 62, Mismatches: 18, Indels: 8
0.70 0.20 0.09
Matches are distributed among these distances:
34 1 0.02
35 6 0.10
36 49 0.79
37 5 0.08
38 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (36 bp):
TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAA
Found at i:2877333 original size:72 final size:74
Alignment explanation
Indices: 2877181--2877338 Score: 221
Period size: 72 Copynumber: 2.1 Consensus size: 74
2877171 AATAGTCTTG
* *
2877181 AGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGTGAGACAAAGTCTGTTTTAAGAA
1 AGTGAAAT-AAAT-CCTTCTTTCGAGTGAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGAA
* **
2877246 AAGCAAACTTG
64 AAACAAACTCA
2877257 AGTGAAATAAAT-CTTCTTTCGAGT-AAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGAAAA
1 AGTGAAATAAATCCTTCTTTCGAGTGAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGAAAA
*
2877320 ACAATCTCA
66 ACAAACTCA
*
2877329 AGTGAGATAA
1 AGTGAAATAA
2877339 TCATCTGCAT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
72 51 0.68
73 12 0.16
75 4 0.05
76 8 0.11
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (74 bp):
AGTGAAATAAATCCTTCTTTCGAGTGAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGAAAA
ACAAACTCA
Found at i:2884263 original size:36 final size:36
Alignment explanation
Indices: 2884206--2884661 Score: 163
Period size: 36 Copynumber: 13.4 Consensus size: 36
2884196 TCAAAGTTTA
* * * *
2884206 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
2884242 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
** * * * *
2884278 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGAGAGACAAAATT
* * *
2884306 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
2884343 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
** * * * *
2884379 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGAGAGACAAAATT
* *
2884407 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACCT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
* * ** * * *
2884445 AGTTCCAAAAGAAAATGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
* * * *
2884481 TGTTTAAAGGAAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAAAC-TATCTCAAGAGAGACAAAATT
* * *
2884510 TGTTTCAAGAGAAACTATCTTAAGAGAGAGAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
** * * * *
2884546 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGAGAGACAAAATT
* * * *
2884574 ATGTATCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
*
2884612 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
*
2884648 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
2884662 TTTTTTCAAT
Statistics
Matches: 293, Mismatches: 83, Indels: 88
0.63 0.18 0.19
Matches are distributed among these distances:
28 8 0.03
29 57 0.19
30 7 0.02
31 2 0.01
32 5 0.02
33 5 0.02
34 3 0.01
35 7 0.02
36 136 0.46
37 60 0.20
38 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:2884326 original size:101 final size:101
Alignment explanation
Indices: 2884191--2884559 Score: 472
Period size: 101 Copynumber: 3.6 Consensus size: 101
2884181 CAAATGTAAC
* * *
2884191 TGTTTTCAAAGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA
1 TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
2884256 CTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
66 CTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
* * *
2884292 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA
1 TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
2884357 CTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
66 CTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
* * * * **
2884393 TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACCTAGTTCCAAAAGAA
1 TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAA
* * * ** * *
2884458 AATGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAA
65 ACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
* * * * **
2884495 CAG-ATTCAAAGATTT-TGTTTCAAGAGAAACTATCTTAAGAGAGAGAAAATTCATTTCAAGGGA
1 -TGTTTTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGA
2884558 AA
64 AA
2884560 TGTTTTCAAT
Statistics
Matches: 238, Mismatches: 27, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
101 156 0.66
102 78 0.33
103 4 0.02
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (101 bp):
TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
CTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
Found at i:2884612 original size:102 final size:103
Alignment explanation
Indices: 2884501--2884706 Score: 333
Period size: 102 Copynumber: 2.0 Consensus size: 103
2884491 AAAACAGATT
* *
2884501 CAAAGATTTTGTTTCAAGAGAAACTATCTTAAGAGAGAGAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
*
2884566 CAATGTTTATGTATCAAGAGAAACTGTCTCAAGGGAGA
66 CAATGTTTATGTATCAAGAGAAACTGTCTCAAGAGAGA
* * * *
2884604 CAAA-ATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAATTTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
*
2884668 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
66 CAATGTTTATGTATCAAGAGAAACTGTCTCAAGAGAGA
2884706 C
1 C
2884707 GAAACCTAGT
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 91 0.96
103 4 0.04
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (103 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
CAATGTTTATGTATCAAGAGAAACTGTCTCAAGAGAGA
Found at i:2884635 original size:167 final size:166
Alignment explanation
Indices: 2884341--2884710 Score: 488
Period size: 167 Copynumber: 2.2 Consensus size: 166
2884331 GGAGACAAAA
* *
2884341 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTT
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGAGAAAATTCATTTCAAGGGAAATGTTTTCAATGTT
* * *
2884406 TATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACCTAGTTCCAAAAGAAAATGTCTCAAGGG
66 TATGTATCAAGAGAAACTATCTCAAGAGAGACAAAACCTAGTTCCAAAAGAAAATATCTCAAGAG
*
2884471 AGACAAAATTTGTTTAAAGGAAAACAGATTCAAAGAT
131 AGACAAAATTTATTTAAAGGAAAACAGATTCAAAG-T
*
2884508 TTTGTTTCAAGAGAAACTATCTTAAGAGAGAGAAAATTCATTTCAAGGGAAATGTTTTCAATGTT
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGAGAAAATTCATTTCAAGGGAAATGTTTTCAATGTT
* * ** * * ** **
2884573 TATGTATCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCTCAAGAG
66 TATGTATCAAGAGAAACTATCTCAAGAGAGACAAAACCTAGTTCCAAAAGAAAATATCTCAAGAG
* * **** *
2884638 AGACAAAATTTATTTCAAGGGAAATTTTTTCAATGT
131 AGACAAAATTTATTTAAAGGAAAACAGATTCAAAGT
*
2884674 TTATGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
1 TT-TGTTTCAAGAGAAACTATCTCAAGAGAGA-GAAA
2884711 CCTAGTTCTA
Statistics
Matches: 175, Mismatches: 26, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
166 3 0.02
167 168 0.96
168 4 0.02
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (166 bp):
TTTGTTTCAAGAGAAACTATCTCAAGAGAGAGAAAATTCATTTCAAGGGAAATGTTTTCAATGTT
TATGTATCAAGAGAAACTATCTCAAGAGAGACAAAACCTAGTTCCAAAAGAAAATATCTCAAGAG
AGACAAAATTTATTTAAAGGAAAACAGATTCAAAGT
Found at i:2884735 original size:102 final size:102
Alignment explanation
Indices: 2884511--2884758 Score: 300
Period size: 102 Copynumber: 2.4 Consensus size: 102
2884501 CAAAGATTTT
* * * * *
2884511 GTTTCAAGAGAAACTATCTTAAGAGAGAGAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
1 GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTAT
* ** *
2884576 GTATCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
66 GTATCAAGAGAAACTGTCTCAAGAGAGACAAAACCTA
** ** *
2884613 GTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAATTTTTTCAATGTTTAT
1 GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTAT
* *
2884678 GTTTCAAGAGAAACTGTCTCAAGAGAGACGAAACCTA
66 GTATCAAGAGAAACTGTCTCAAGAGAGACAAAACCTA
* * * *
2884715 G-TTCTAAAAGAAAATGTCTCAAGGGAGATAAAATTTGTTTCAAG
1 GTTTC-AAAAGAAAATATCTCAAGAGAGACAAAATTTATTTCAAG
2884759 AGAGACAAAA
Statistics
Matches: 125, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
101 3 0.02
102 122 0.98
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (102 bp):
GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTAT
GTATCAAGAGAAACTGTCTCAAGAGAGACAAAACCTA
Found at i:2884904 original size:72 final size:75
Alignment explanation
Indices: 2884787--2884929 Score: 229
Period size: 72 Copynumber: 1.9 Consensus size: 75
2884777 AAAAAATAGT
* *
2884787 CTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGTGAGACAAAGTCTGTTTTA
1 CTTGAGTGAAATGAAAT-CCTTCTTTCGAGTGAAAACAGTCTCAAGTGAGACAAAGTATGTTTTA
2884852 AGAAAAGCAAA
65 AGAAAAGCAAA
*
2884863 CTTGAGTGAAAT-AAAT-CTTCTTTCGAGT-AAAACAGTCTCAAGTGAGATAAAGTATGTTTTAA
1 CTTGAGTGAAATGAAATCCTTCTTTCGAGTGAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAA
2884925 GAAAA
66 GAAAA
2884930 AATAATCTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
72 36 0.56
73 12 0.19
75 4 0.06
76 12 0.19
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (75 bp):
CTTGAGTGAAATGAAATCCTTCTTTCGAGTGAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAA
GAAAAGCAAA
Found at i:2893672 original size:3 final size:3
Alignment explanation
Indices: 2893664--2893707 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2893654 AAAGTAATCG
2893664 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2893708 ATATATTAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2894771 original size:29 final size:30
Alignment explanation
Indices: 2894722--2894779 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
2894712 GGACGGAGCT
2894722 AGAAAAATAAATTTGACGTGTCAAATTTAG
1 AGAAAAATAAATTTGACGTGTCAAATTTAG
*
2894752 AGAAAAAT-ATTTTGGA-GTGTCAAATTTA
1 AGAAAAATAAATTT-GACGTGTCAAATTTA
2894780 AAAATTGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (30 bp):
AGAAAAATAAATTTGACGTGTCAAATTTAG
Found at i:2906201 original size:15 final size:15
Alignment explanation
Indices: 2906177--2906212 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2906167 ACACTATTAA
*
2906177 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
2906192 ATTAAATTATAAAGT
1 ATTAAATTATAAAAT
2906207 ATTAAA
1 ATTAAA
2906213 CATATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:2906246 original size:22 final size:22
Alignment explanation
Indices: 2906186--2906258 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
2906176 AATTAATTTA
*
2906186 TAAAATATTAAATTATAAAGT-AT
1 TAAAATA-TAAA-TATAAATTAAT
*
2906209 TAAACATATAATTATAAATTAAT
1 TAAA-ATATAAATATAAATTAAT
* *
2906232 TAAAATCTAAATATAATTTAAT
1 TAAAATATAAATATAAATTAAT
2906254 TAAAA
1 TAAAA
2906259 CACAATATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
22 27 0.63
23 13 0.30
24 3 0.07
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (22 bp):
TAAAATATAAATATAAATTAAT
Found at i:2908416 original size:3 final size:3
Alignment explanation
Indices: 2908408--2908456 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2908398 AACTAATGTT
2908408 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2908456 T
1 T
2908457 ATTTTAATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2908501 original size:23 final size:23
Alignment explanation
Indices: 2908446--2908503 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
2908436 TATTATTATT
*
2908446 ATTATTATTATA-TTTTAATTAA
1 ATTATAATTATATTTTTAATTAA
* * *
2908468 ATTACATTTATATTTTTAGTTAA
1 ATTATAATTATATTTTTAATTAA
*
2908491 TTTATAATTATAT
1 ATTATAATTATAT
2908504 GCTTATTACT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTATAATTATATTTTTAATTAA
Found at i:2910384 original size:16 final size:16
Alignment explanation
Indices: 2910363--2910406 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
2910353 ATCAAGACGA
2910363 AGGAAACTACTTTTCG
1 AGGAAACTACTTTTCG
2910379 AGGAAACTACTTTTCG
1 AGGAAACTACTTTTCG
* *
2910395 AGCAAACAACTT
1 AGGAAACTACTT
2910407 GTTCTTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (16 bp):
AGGAAACTACTTTTCG
Found at i:2911025 original size:13 final size:13
Alignment explanation
Indices: 2911007--2911042 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2910997 AAAAATGAGT
2911007 AAATAATAATAAA
1 AAATAATAATAAA
2911020 AAATAATAATAAA
1 AAATAATAATAAA
2911033 AAA-AATAATA
1 AAATAATAATA
2911043 TATTATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAATAATAAA
Found at i:2911029 original size:16 final size:15
Alignment explanation
Indices: 2911008--2911042 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2910998 AAAATGAGTA
2911008 AATAATAATAAAAAAT
1 AATAATAA-AAAAAAT
2911024 AATAATAAAAAAAAT
1 AATAATAAAAAAAAT
2911039 AATA
1 AATA
2911043 TATTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAATAAAAAAAAT
Done.