Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 11 of 362
Found at i:3687998 original size:135 final size:128
Alignment explanation
Indices: 3687705--3688155 Score: 322
Period size: 135 Copynumber: 3.5 Consensus size: 128
3687695 ATTTTTTAGA
* * * * * ** * *
3687705 AAAAAACGCCGCTAAAGACCACGATCTTTAGCGGCGTTTTTATAAACGCGCCGCTAA-AGACCAG
1 AAAAAGCGCCGCTATAGACCAAGAACTTTAGCGGCTTTTTTATAAAAACGCCGCTAATAGTCCTG
* ** * * * *
3687769 GACCTTTAGCGGCGCTCT-TA-AAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCG-TTTTTT
66 G-TCTTGGGCGGCGTTTTGTACAAAAGCGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTAT
** ** *** * ** *
3687830 ATAAAAGCGCCGCTA-ATGTTCTTGGTGTATAGCGGCATTTTTTATAAATGCGCCGCTAATATTC
1 A-AAAAGCGCCGCTATA-GACCAAGAACTTTAGCGGC-TTTTTTATAAAAACGCCGCTAATAGTC
* * *
3687894 TTGGTCTATAGCGGCGTCGGCGTTTTTTATAAAAGCGCCGCTAAAGACCAGGACCTTTAGCGGCG
63 CTGGTCT-T---GG-G-CGGCGTTTTGTACAAAAGCGCCGCTAAAGACCAGGACCTTTAGCGGCG
3687959 CTTTTAT
122 CTTTTAT
* ** * *
3687966 AAAAAGCGCCGCTATACACCAAGAACTTTAGCGGCGCTTTTATAAAAAAAGCCGCTACA-GGTCC
1 AAAAAGCGCCGCTATAGACCAAGAACTTTAGCGGCTTTTTTAT-AAAAACGCCGCTA-ATAGTCC
* * * *
3688030 TGGTCTTTGGCGGCGTTTTGTACAAAAGCGCCGCTATAGACCAAGAACTTTAGC-GCGCTTTAAT
64 TGGTCTTGGGCGGCGTTTTGTACAAAAGCGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTT--T
*
3688094 AA
127 AT
* * *
3688096 AAAAAACGCCGCTATAGACCAAGAACATTAGCGGCGCTTTTTTAAAAAAACGCCGCTAAT
1 AAAAAGCGCCGCTATAGACCAAGAACTTTAGC-G-GCTTTTTTATAAAAACGCCGCTAAT
3688156 TTGCCTAGTT
Statistics
Matches: 253, Mismatches: 52, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
125 2 0.01
126 24 0.09
127 22 0.09
128 12 0.05
129 39 0.15
130 33 0.13
131 14 0.06
132 8 0.03
133 7 0.03
134 9 0.04
135 75 0.30
136 8 0.03
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (128 bp):
AAAAAGCGCCGCTATAGACCAAGAACTTTAGCGGCTTTTTTATAAAAACGCCGCTAATAGTCCTG
GTCTTGGGCGGCGTTTTGTACAAAAGCGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTAT
Found at i:3688057 original size:86 final size:87
Alignment explanation
Indices: 3687948--3688109 Score: 249
Period size: 86 Copynumber: 1.9 Consensus size: 87
3687938 AGACCAGGAC
*
3687948 CTTTAGCGGCGCTTTTATAAAAAGCGCCGCTATACACCAAGAACTTTAGCGGCGCTTTTAT-AAA
1 CTTTAGCGGCGCTTTTATAAAAAGCGCCGCTATACACCAAGAACTTTAGC-GCGCTTTAATAAAA
3688012 AAAA-GCCGCTACAGGTCCTGGT
65 AAAACGCCGCTACAGGTCCTGGT
* * *
3688034 CTTTGGCGGCG-TTTTGTACAAAAGCGCCGCTATAGACCAAGAACTTTAGCGCGCTTTAATAAAA
1 CTTTAGCGGCGCTTTTATA-AAAAGCGCCGCTATACACCAAGAACTTTAGCGCGCTTTAATAAAA
3688098 AAAACGCCGCTA
65 AAAACGCCGCTA
3688110 TAGACCAAGA
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
85 15 0.22
86 47 0.68
87 7 0.10
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (87 bp):
CTTTAGCGGCGCTTTTATAAAAAGCGCCGCTATACACCAAGAACTTTAGCGCGCTTTAATAAAAA
AAACGCCGCTACAGGTCCTGGT
Found at i:3688475 original size:21 final size:21
Alignment explanation
Indices: 3688451--3688495 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
3688441 TCCTGTTCTG
3688451 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
3688472 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
3688493 CTC
1 CTC
3688496 TGCTCTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.58, G:0.18, T:0.24
Consensus pattern (21 bp):
CTCCGCCTCCCTCGCTGCTGC
Found at i:3689085 original size:18 final size:18
Alignment explanation
Indices: 3689053--3689090 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3689043 TACAATATAG
3689053 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
3689072 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
3689089 TA
1 TA
3689091 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:3694665 original size:21 final size:21
Alignment explanation
Indices: 3694641--3694680 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3694631 AAATTAATTC
*
3694641 ATACTTAAGTTGAATCAAATA
1 ATACTTAAGTTGAACCAAATA
3694662 ATACTTAAGTTGAACCAAA
1 ATACTTAAGTTGAACCAAA
3694681 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (21 bp):
ATACTTAAGTTGAACCAAATA
Found at i:3696852 original size:133 final size:133
Alignment explanation
Indices: 3696614--3697131 Score: 1018
Period size: 133 Copynumber: 3.9 Consensus size: 133
3696604 GAATTCAACA
*
3696614 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACATTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
3696679 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
3696744 ATT
131 ATT
*
3696747 ATATAAAACGTGAACAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
3696812 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
3696877 ATT
131 ATT
3696880 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
3696945 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
3697010 ATT
131 ATT
3697013 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
3697078 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
3697132 GGAATCACCA
Statistics
Matches: 382, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 382 1.00
ACGTcount: A:0.52, C:0.18, G:0.10, T:0.20
Consensus pattern (133 bp):
ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
ATT
Found at i:3700910 original size:36 final size:38
Alignment explanation
Indices: 3700869--3700944 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
3700859 CTTCAATTAC
* * *
3700869 TAGTTAACTCCTAAACC-G-TAAATCTTAAACCATATA
1 TAGTTAACTCATAAACCTGCTAAACCCTAAACCATATA
3700905 TAGTTAACTCATAAACCTGCTTAAACCCTAAACCATATA
1 TAGTTAACTCATAAACCTGC-TAAACCCTAAACCATATA
3700944 T
1 T
3700945 CTTAAACTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 16 0.47
37 1 0.03
39 17 0.50
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (38 bp):
TAGTTAACTCATAAACCTGCTAAACCCTAAACCATATA
Found at i:3701455 original size:41 final size:40
Alignment explanation
Indices: 3701124--3701455 Score: 394
Period size: 41 Copynumber: 8.1 Consensus size: 40
3701114 GTTCTATGAC
*
3701124 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GT
* * *
3701165 TTTTAGCGGTGTTTTACCGAAAGTGCCGCTAATGCTCTGTT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTG-T
3701206 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GT
*
3701247 TTTTAGCGGTGTTTTACCCAAAGCGCCGCTAATGCTCTGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
* * *
3701287 GTTTTAGCGGCGTTTTACCCGAAGCACCGCTAATGATCTGGT
1 -TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GT
* *
3701329 TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGATCTGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
* *** * ** *
3701369 TTTTAGAGGCGTTTTAGTAAAAAACGCCGCTGTTGCTCTAT
1 TTTTAGCGGCGTTTTA-CCCAAAGCGCCGCTAATGCTCTGT
* ** * *
3701410 TTTTAGCGGCGTTTTTCTTAAAACGCCGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
3701450 ATTTTA
1 -TTTTA
3701456 AAATTTTTGC
Statistics
Matches: 255, Mismatches: 30, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
40 39 0.15
41 213 0.84
42 3 0.01
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
Found at i:3701931 original size:23 final size:22
Alignment explanation
Indices: 3701905--3701948 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3701895 CAATAACAGC
*
3701905 ATGCAGATAAACTGTAGGTAAAA
1 ATGCAGACAAACTGTA-GTAAAA
*
3701928 ATGCAGACACACTGTAGTAAA
1 ATGCAGACAAACTGTAGTAAA
3701949 GATGTGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (22 bp):
ATGCAGACAAACTGTAGTAAAA
Found at i:3705487 original size:27 final size:27
Alignment explanation
Indices: 3705448--3705907 Score: 560
Period size: 27 Copynumber: 17.0 Consensus size: 27
3705438 TAGAATACTT
** *
3705448 TAGTTTACCAAATTACCAGAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* * * *
3705475 TGGTTTGTAAAATTACTAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
*
3705502 TAGTTTATAAAATCACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* * **
3705529 TAGTTTGTAAGATTACCAAAATACCTT
1 TAGTTTATAAAATTACCAAAATACCCC
* * *
3705556 TGGTTTACAAAATTACCAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
* * * *
3705583 TGGTTTGTAAAATTACTAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
* *
3705610 TGGTTTATAAAATCACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* * *
3705637 TAATTTGTAAAATTACCAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
*
3705664 TAGTTTACAAAATTACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* *
3705691 TAGTTTATAAAATTACTAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
* *
3705718 TGGTTTATAAAATTACCAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
*
3705745 TAGTTTACAAAATTACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* *
3705772 TAGTTTATAAAATTACTAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
*
3705799 TGGTTTATAAAATTACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* *
3705826 TAATTTGTAAAATTACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* * *
3705853 TGGTTTGTAAAATTATCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* *
3705880 TAGTTTGTTAAATTACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
3705907 T
1 T
3705908 GATTTGTGAA
Statistics
Matches: 372, Mismatches: 61, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 372 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.32
Consensus pattern (27 bp):
TAGTTTATAAAATTACCAAAATACCCC
Found at i:3705928 original size:27 final size:27
Alignment explanation
Indices: 3705457--3705991 Score: 458
Period size: 27 Copynumber: 19.8 Consensus size: 27
3705447 TTAGTTTACC
* *
3705457 AAATTACCAGAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* * *
3705484 AAATTACTAAAATA-CCCTTAGTTTATA
1 AAATTACCAAAATACCCCTGA-TTTGTA
*
3705511 AAATCACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* ** * **
3705538 AGATTACCAAAATACCTTTGGTTTACA
1 AAATTACCAAAATACCCCTGATTTGTA
* *
3705565 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* * * *
3705592 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGATTTGTA
* *
3705619 AAATCACCAAAATACCCCTAATTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* **
3705646 AAATTACCAAAATA-CCCTTAGTTTACA
1 AAATTACCAAAATACCCCTGA-TTTGTA
*
3705673 AAATTACCAAAATACCCCT-AGTTTATA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* * * *
3705700 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGATTTGTA
* **
3705727 AAATTACCAAAATA-CCCTTAGTTTACA
1 AAATTACCAAAATACCCCTGA-TTTGTA
*
3705754 AAATTACCAAAATACCCCT-AGTTTATA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* * * *
3705781 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGATTTGTA
*
3705808 AAATTACCAAAATACCCCTAATTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
*
3705835 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* *
3705862 AAATTATCAAAATACCCCT-AGTTTGTT
1 AAATTACCAAAATACCCCTGA-TTTGTA
*
3705889 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGATTTGTA
* ** **
3705916 AAATAACTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
*** *
3705943 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
* *
3705970 AAATTACCAAAGTACCCTTGAT
1 AAATTACCAAAATACCCCTGAT
3705992 CTACAGAATT
Statistics
Matches: 424, Mismatches: 71, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
26 16 0.04
27 392 0.92
28 16 0.04
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:3706055 original size:27 final size:27
Alignment explanation
Indices: 3706025--3706106 Score: 130
Period size: 27 Copynumber: 3.1 Consensus size: 27
3706015 CGATTTACAA
*
3706025 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
3706052 AATTACCGAAATACCTCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
3706079 AATTATCGAAATACCCCTGTA-GGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
3706105 AA
1 AA
3706107 CTGTAAGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 7 0.14
27 44 0.86
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:3708204 original size:16 final size:16
Alignment explanation
Indices: 3708185--3708230 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3708175 GCAAAATTTT
*
3708185 AAAAAACTAAAAGATA
1 AAAAAACTAAAAAATA
3708201 AAAAAA-TATAAAAATA
1 AAAAAACTA-AAAAATA
*
3708217 TAAAAAC-AAAAAAT
1 AAAAAACTAAAAAAT
3708231 GATCTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (16 bp):
AAAAAACTAAAAAATA
Found at i:3708311 original size:280 final size:280
Alignment explanation
Indices: 3707923--3708434 Score: 864
Period size: 280 Copynumber: 1.8 Consensus size: 280
3707913 TAAAAAACAT
* *
3707923 AAAATATAAAATATAAAAACAAAAAATGATCTAATTGGAGAATCGAAACTAAATCCACAACTTAC
1 AAAATATAAAATATAAAAACAAAAAATGATCTAATTAGAGAATAGAAACTAAATCCACAACTTAC
* * *
3707988 AAATAGTACGAGACTAATAGCATAATTTAATCTTACCAATTTAATTGCTAATGTTTATGCAAGTA
66 AAATAGTACGAGACTAATAGCATAATTTAATCTAACAAATTTAACTGCTAATGTTTATGCAAGTA
*
3708053 CTAGAATTTCAAATTAAAAAAGTAGAATAATTAAAATTGATCAAATAAAACTGAAAGGACTAAAT
131 CTAGAATTTCAAATTAAAAAAGTAGAATAATTAAAATTGATCAAATAAAACTAAAAGGACTAAAT
* *
3708118 CCACAACTTATGTACAGTACAAAGGTTAATAAAAAAATGACTTCTTACCTTATTCCAGCAAAATT
196 CCACAACTTATGAACAGTACAAAGATTAATAAAAAAATGACTTCTTACCTTATTCCAGCAAAATT
3708183 TTAAAAAACTAAAAGATAAA
261 TTAAAAAACTAAAAGATAAA
*
3708203 AAAATATAAAAATATAAAAACAAAAAATGATCTAATTAGAGAATAGGAACTAAATCCACAAC-TA
1 AAAATAT-AAAATATAAAAACAAAAAATGATCTAATTAGAGAATAGAAACTAAATCCACAACTTA
* * *
3708267 CATATAGTACGAGACTAATAGCATAATTTAATCTAATAAATTTAACTGCTATTGTTTATGCAAGT
65 CAAATAGTACGAGACTAATAGCATAATTTAATCTAACAAATTTAACTGCTAATGTTTATGCAAGT
* * *
3708332 ACTAGAATTTCAAATTAAAAAAGTAGAATAATTGAAATTGATTAGATAAAACTAAAAGGACTAAA
130 ACTAGAATTTCAAATTAAAAAAGTAGAATAATTAAAATTGATCAAATAAAACTAAAAGGACTAAA
*
3708397 TCCACAACTTATGAATAGTACAAAGATTAATAAAAAAA
195 TCCACAACTTATGAACAGTACAAAGATTAATAAAAAAA
3708435 ATTCAATCGT
Statistics
Matches: 215, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
280 164 0.76
281 51 0.24
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (280 bp):
AAAATATAAAATATAAAAACAAAAAATGATCTAATTAGAGAATAGAAACTAAATCCACAACTTAC
AAATAGTACGAGACTAATAGCATAATTTAATCTAACAAATTTAACTGCTAATGTTTATGCAAGTA
CTAGAATTTCAAATTAAAAAAGTAGAATAATTAAAATTGATCAAATAAAACTAAAAGGACTAAAT
CCACAACTTATGAACAGTACAAAGATTAATAAAAAAATGACTTCTTACCTTATTCCAGCAAAATT
TTAAAAAACTAAAAGATAAA
Found at i:3708830 original size:19 final size:19
Alignment explanation
Indices: 3708806--3708867 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
3708796 AATCTTTAAG
3708806 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
3708825 GATATGCAGTCTTAGATAT
1 GATATGCAATCTTAGATAT
3708844 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
3708865 GAT
1 GAT
3708868 CTTGTAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 30 0.77
21 9 0.23
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3715346 original size:44 final size:44
Alignment explanation
Indices: 3715294--3716001 Score: 541
Period size: 44 Copynumber: 16.1 Consensus size: 44
3715284 CAAGATTTGG
*
3715294 CATCCCTGTTTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * *** *** *
3715338 CA-CTCCTGTGCTTACAACAAAGCAGATCGAAGATTTTAG--CATGG
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * * *
3715382 CATCCCTGTGTTTATAGGGACCA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
* *
3715426 CATCCCTATATTTATAGGGAACAGATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * * ** * *
3715470 CA-CTCCTATGCTTACAGCGAAGCAGATCAAAGATTTCAG-TATGG
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATCTGA
* * * *
3715514 CATCCCTGTGCTTATAGGGAACA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
3715558 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * ** *
3715602 CA-CTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG--CATGG
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * * *
3715646 CATCCCTGTGTTTATAGGGAACA-AGTTGAAAATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
* * *
3715690 CATCCCTGTGTTTATAGGGAACAAATTGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * ** *
3715734 CATTCCTGTGATTATAGCGAAGCAAATCGAAGATTTCAG--CATGG
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * *
3715778 CATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
*
3715822 CATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * ** ** *
3715866 CATTCCTATGCTTATAGTAAAGCAGATCGAAGATTTCAG-TATGA
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATCTGA
* * *
3715910 CATCCTTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGGA
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCT-GA
* * *
3715955 -ATCCCTGTATTTATAGGGAACAAATCGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
3715998 CATC
1 CATC
3716002 TCCATTTCGA
Statistics
Matches: 523, Mismatches: 107, Indels: 68
0.75 0.15 0.10
Matches are distributed among these distances:
42 5 0.01
43 65 0.12
44 372 0.71
45 81 0.15
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
Found at i:3715523 original size:132 final size:132
Alignment explanation
Indices: 3715286--3716004 Score: 1141
Period size: 132 Copynumber: 5.4 Consensus size: 132
3715276 CAAAGAAACA
* *
3715286 AGATTTGGCATCCCTGTTTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* * * *
3715351 ACAACAAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGACCAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3715416 GC
131 GC
* * * *
3715418 AGATTTGGCATCCCTATATTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* * *
3715483 ACAGCGAAGCAGATCAAAGATTTCAGTATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3715548 GC
131 GC
*
3715550 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
*
3715615 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAAATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3715680 GC
131 GC
* * * *
3715682 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAACAGATCTGACATTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* *
3715747 ATAGCGAAGCAAATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3715812 GC
131 GC
* *
3715814 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* ** * * *
3715879 ATAGTAAAGCAGATCGAAGATTTCAGTATGACATCCTTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3715944 GC
131 GC
* * *
3715946 AGATTTGGAATCCCTGTATTTATAGGGAACAAATCGAAGATAACAGATCTGACATCTCC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACA-CTCC
3716005 ATTTCGACGG
Statistics
Matches: 547, Mismatches: 39, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
132 544 0.99
133 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GC
Found at i:3716599 original size:19 final size:19
Alignment explanation
Indices: 3716575--3716672 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
3716565 AATCTTTAAG
3716575 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3716594 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3716613 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3716630 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3716649 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
3716670 GAT
1 GAT
3716673 CTTGTAATCT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3716605 original size:36 final size:35
Alignment explanation
Indices: 3716565--3716672 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 35
3716555 ATGGAAATAT
3716565 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
3716601 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
3716637 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
3716673 CTTGTAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 28 0.46
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:3719721 original size:12 final size:12
Alignment explanation
Indices: 3719704--3719743 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
3719694 CATACACGCG
*
3719704 CGTGTGCCAGGC
1 CGTGTGCTAGGC
3719716 CGTGTGCTAGGC
1 CGTGTGCTAGGC
*
3719728 CATGTGCTAGGC
1 CGTGTGCTAGGC
3719740 CGTG
1 CGTG
3719744 CCGAACCTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.10, C:0.28, G:0.40, T:0.23
Consensus pattern (12 bp):
CGTGTGCTAGGC
Found at i:3727537 original size:6 final size:6
Alignment explanation
Indices: 3727526--3727550 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3727516 ATATATTTAT
3727526 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
3727551 AAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:3731054 original size:14 final size:13
Alignment explanation
Indices: 3731020--3731069 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
3731010 GTACAAATTG
3731020 TATATATATTATTT
1 TATATATATTA-TT
*
3731034 TTTATATATTATT
1 TATATATATTATT
*
3731047 TAT-CATATTATT
1 TATATATATTATT
3731059 TATAT-TATTAT
1 TATATATATTAT
3731070 ACATTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 17 0.55
13 4 0.13
14 10 0.32
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATATATTATT
Found at i:3731064 original size:21 final size:21
Alignment explanation
Indices: 3731038--3731083 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3731028 TTATTTTTTA
3731038 TATATTATT-TATCATATTATT
1 TATATTATTATA-CATATTATT
*
3731059 TATATTATTATACATTTTATT
1 TATATTATTATACATATTATT
3731080 TATA
1 TATA
3731084 AATTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTATTATACATATTATT
Found at i:3731114 original size:19 final size:19
Alignment explanation
Indices: 3731079--3731115 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3731069 TACATTTTAT
*
3731079 TTATAAATTTTATTATATG
1 TTATAAATTTTACTATATG
*
3731098 TTATAAATTTTCCTATAT
1 TTATAAATTTTACTATAT
3731116 ATATATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (19 bp):
TTATAAATTTTACTATATG
Found at i:3731734 original size:71 final size:67
Alignment explanation
Indices: 3731620--3731775 Score: 199
Period size: 71 Copynumber: 2.3 Consensus size: 67
3731610 GTTATTTTAA
* * * *
3731620 GTTATATTTGCATAAAATATTGTTATATATTATGTAATTTATATTGTTAT-ATTCATTGTTTTCT
1 GTTATATTTGCATGAAATATTATTATATATTATGTAATCTATATCGTTATGA-TCATTGTTTTCT
3731684 AT-
65 ATG
3731686 GTTATATTTTGCATGAAATATTATTATTTATGCATTATGTAATCTATATCGTTATGATCATTGTT
1 GTTATA-TTTGCATGAAATATTATTA--TAT--ATTATGTAATCTATATCGTTATGATCATTGTT
3731751 TTCTATG
61 TTCTATG
*
3731758 GTTATATATGCATGAAAT
1 GTTATATTTGCATGAAAT
3731776 GATGATGCAT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
66 6 0.08
67 17 0.22
69 3 0.04
71 45 0.58
72 7 0.09
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (67 bp):
GTTATATTTGCATGAAATATTATTATATATTATGTAATCTATATCGTTATGATCATTGTTTTCTA
TG
Found at i:3739172 original size:46 final size:46
Alignment explanation
Indices: 3739092--3739255 Score: 222
Period size: 46 Copynumber: 3.6 Consensus size: 46
3739082 TTTGACATGA
* * * *
3739092 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
* * * *
3739138 TTCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
3739184 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
3739230 TGCCATGGTATCTTTCAACCATGGTC
1 TGCCATGGTATCTTTCAACCATGGTC
3739256 ATATCAGGTT
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
45 4 0.04
46 99 0.96
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:3739238 original size:30 final size:33
Alignment explanation
Indices: 3739202--3739273 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 33
3739192 TATCTTTCAA
*
3739202 CCATGGTCTTAC-A-CAT-TTCATATCAGGTTG
1 CCATGGTCTTACAACCATGGTCATATCAGGTTG
*
3739232 CCATGGTATCTTTCAACCATGGTCATATCAGGTTG
1 CCATGG--TCTTACAACCATGGTCATATCAGGTTG
3739267 CCATGGT
1 CCATGGT
3739274 ATATTTCAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
30 6 0.17
32 5 0.14
33 2 0.06
34 3 0.09
35 19 0.54
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (33 bp):
CCATGGTCTTACAACCATGGTCATATCAGGTTG
Found at i:3739265 original size:35 final size:35
Alignment explanation
Indices: 3739219--3739290 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
3739209 CTTACACATT
*
3739219 TCATATCAGGTTGCCATGGTATCTTTCAACCATGG
1 TCATATCAGGTTGCCATGGTATATTTCAACCATGG
3739254 TCATATCAGGTTGCCATGGTATATTTCAACCATGG
1 TCATATCAGGTTGCCATGGTATATTTCAACCATGG
3739289 TC
1 TC
3739291 TTACACATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (35 bp):
TCATATCAGGTTGCCATGGTATATTTCAACCATGG
Found at i:3741267 original size:20 final size:21
Alignment explanation
Indices: 3741238--3741278 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3741228 ACATATTTGA
3741238 TTTTCCCTTTTT-TTTCTTTC
1 TTTTCCCTTTTTCTTTCTTTC
*
3741258 TTTTCTCTTTTTCTTTCTTTC
1 TTTTCCCTTTTTCTTTCTTTC
3741279 CTTCCCCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCCCTTTTTCTTTCTTTC
Found at i:3747773 original size:44 final size:44
Alignment explanation
Indices: 3746961--3747758 Score: 1107
Period size: 44 Copynumber: 18.1 Consensus size: 44
3746951 TCACCGATAG
*
3746961 CAGATTTGGCGTCTCTGTATTGATAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
3747005 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCATATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * *
3747049 TAGATTTGGCGCCTCTGTATTGACAGAGAGCAAATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * * *
3747093 TAGATTTCGCGTTTCTGTATTGACAGAGAGCAGATCAAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
3747137 CAAATTTGGCGTCTCTGTATTGACAGTGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * * * *
3747181 CAAATTCGGTGTCTCTATATTGACAGAGAGCAGATCTAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
*
3747225 CAGATTTGGCGTCTCTGTATTGACAGAGGGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * * * *
3747269 CAGATTTGGCGTCTCTGTATTGACAAAGGGCAGATTGAAAATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
** *
3747313 CAGATTTAACGTCTCTATATTGACAGAGAGCAGATCGAAGAT-A
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
3747356 GCAGATTTGACGTCTCTGTATTGACAGAGATCAGATCGAAGAT-A
1 -CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
**
3747400 GCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATTAAAGATGA
1 -CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * *
3747445 CAGATTTGGCGTTTCTGTATTAACAGTGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * * * *
3747489 CAGATTTGACATCTCTGTATTGACAGAGAGCAGATCTAAGAGGT
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
3747533 CAGATTTGGCGTCTCTGTATTGATAGAGAGCAGATCAAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * *
3747577 CAGATTTGGCATCTCTGTATTGACAGAGGGCAGATTGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
*
3747621 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
*
3747665 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGAT-A
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * * *
3747708 GCAGATTTGACGTCTCTGTATTGACAGAGGGCAGGTCAAAGATGA
1 -CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
3747753 CAGATT
1 CAGATT
3747759 CGGTTTCTCC
Statistics
Matches: 669, Mismatches: 81, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
43 2 0.00
44 665 0.99
45 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
Found at i:3747828 original size:132 final size:132
Alignment explanation
Indices: 3746961--3747852 Score: 735
Period size: 132 Copynumber: 6.8 Consensus size: 132
3746951 TCACCGATAG
* * * * * * *
3746961 CAGATTTGGCGTCTCTGTATTGATAGAGAGCAGATCGAAGATGACAGATTTGGCGTCTCTGTATT
1 CAGATTCGGCGTCTCCGTATTGACAGAGAGCAGATCAAAGATAACAGACTTGGCATCTCTGTATT
* * * * ** * * *
3747026 GGCAGAGAGCATATCGAAGAT-GATAGATTTGGCGCCTCTGTATTGACAGAGAGCAAATCGAAGA
66 GACAGAGAGCAGATCGAAGATAG-CAGATTTGACATCTCTGTATTGACAGAGGGCAGATCAAAGA
3747090 TGA
130 TGA
* * * * * * *
3747093 TAGATTTC-GCGTTTCTGTATTGACAGAGAGCAGATCAAAGATGACAAATTTGGCGTCTCTGTAT
1 CAGA-TTCGGCGTCTCCGTATTGACAGAGAGCAGATCAAAGATAACAGACTTGGCATCTCTGTAT
* * * *** * * *
3747157 TGACAGTGAGCAGATCGAAGAT-GACAAATTCGGTGTCTCTATATTGACAGAGAGCAGATCTAAG
65 TGACAGAGAGCAGATCGAAGATAG-CAGATTTGACATCTCTGTATTGACAGAGGGCAGATCAAAG
3747221 ATGA
129 ATGA
* * * * * * *
3747225 CAGATTTGGCGTCTCTGTATTGACAGAGGGCAGATCGAAGATGACAGATTTGGCGTCTCTGTATT
1 CAGATTCGGCGTCTCCGTATTGACAGAGAGCAGATCAAAGATAACAGACTTGGCATCTCTGTATT
* * * * * * * * * *
3747290 GACAAAGGGCAGATTGAAAATAACAGATTTAACGTCTCTATATTGACAGAGAGCAGATCGAAGAT
66 GACAGAGAGCAGATCGAAGATAGCAGATTTGACATCTCTGTATTGACAGAGGGCAGATCAAAGAT
3747355 -A
131 GA
* * * * * * * *
3747356 GCAGATTTGACGTCTCTGTATTGACAGAGATCAGATCGAAGATAGCAGATTTGGCGTCTCTGTAT
1 -CAGATTCGGCGTCTCCGTATTGACAGAGAGCAGATCAAAGATAACAGACTTGGCATCTCTGTAT
** * * * * * * *
3747421 TGACAGAGAGCAGATTAAAGAT-GACAGATTTGGCGTTTCTGTATTAACAGTGAGCAGATCGAAG
65 TGACAGAGAGCAGATCGAAGATAG-CAGATTTGACATCTCTGTATTGACAGAGGGCAGATCAAAG
3747485 ATGA
129 ATGA
* * * * * *** * *
3747489 CAGATTTGACATCTCTGTATTGACAGAGAGCAGATCTAAGAGGTCAGATTTGGCGTCTCTGTATT
1 CAGATTCGGCGTCTCCGTATTGACAGAGAGCAGATCAAAGATAACAGACTTGGCATCTCTGTATT
* * * **
3747554 GATAGAGAGCAGATCAAAGAT-GACAGATTTGGCATCTCTGTATTGACAGAGGGCAGATTGAAGA
66 GACAGAGAGCAGATCGAAGATAG-CAGATTTGACATCTCTGTATTGACAGAGGGCAGATCAAAGA
3747618 TGA
130 TGA
* * * *
3747621 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATT
1 CAGATTCGGCGTCTCCGTATTGACAGAGAGCAGATCAAAGATAACAGACTTGGCATCTCTGTATT
* *
3747686 GACAGAGAGCAGATCGAAGATAGCAGATTTGACGTCTCTGTATTGACAGAGGGCAGGTCAAAGAT
66 GACAGAGAGCAGATCGAAGATAGCAGATTTGACATCTCTGTATTGACAGAGGGCAGATCAAAGAT
3747751 GA
131 GA
** * * ** *
3747753 CAGATTCGGTTTCTCCGTATTAGGCA-AGGAGTAGATCAAAGATTTCAG-CTTGGCGT-TCCTG-
1 CAGATTCGGCGTCTCCGTATT-GACAGA-GAGCAGATCAAAGATAACAGACTTGGCATCT-CTGT
* * *
3747814 AGTTTG-CAGGGAGCAGGTTGAAGATAGCAGATTTGACAT
63 A--TTGACAGAGAGCAGATCGAAGATAGCAGATTTGACAT
3747853 TCCTGAGTTA
Statistics
Matches: 654, Mismatches: 94, Indels: 24
0.85 0.12 0.03
Matches are distributed among these distances:
131 5 0.01
132 623 0.95
133 26 0.04
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (132 bp):
CAGATTCGGCGTCTCCGTATTGACAGAGAGCAGATCAAAGATAACAGACTTGGCATCTCTGTATT
GACAGAGAGCAGATCGAAGATAGCAGATTTGACATCTCTGTATTGACAGAGGGCAGATCAAAGAT
GA
Found at i:3749345 original size:14 final size:13
Alignment explanation
Indices: 3749311--3749360 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
3749301 GTACAAATTG
3749311 TATATATATTATTT
1 TATATATATTA-TT
*
3749325 TTTATATATTATT
1 TATATATATTATT
*
3749338 TAT-CATATTATT
1 TATATATATTATT
3749350 TATAT-TATTAT
1 TATATATATTAT
3749361 ACATTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 17 0.55
13 4 0.13
14 10 0.32
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATATATTATT
Found at i:3749355 original size:21 final size:21
Alignment explanation
Indices: 3749329--3749374 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3749319 TTATTTTTTA
3749329 TATATTATT-TATCATATTATT
1 TATATTATTATA-CATATTATT
*
3749350 TATATTATTATACATTTTATT
1 TATATTATTATACATATTATT
3749371 TATA
1 TATA
3749375 AATTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTATTATACATATTATT
Found at i:3750028 original size:71 final size:69
Alignment explanation
Indices: 3749908--3750063 Score: 194
Period size: 71 Copynumber: 2.3 Consensus size: 69
3749898 GTTATTTTAA
* * *
3749908 GTTATATTTGCAT-AAA-ATATTGTTATATATTATGTAATTTATATTGTTAT-ATTCATTGTTTT
1 GTTATATTTGCATGAAATATATTATTATATATTATGTAATCTATATCGTTATGA-TCATTGTTTT
3749970 CTAT-
65 CTATG
* *
3749974 GTTATATTTTGCATGAAATATTATTATGTATGTATTTTGTAATCTATATCGTTATGATCATTGTT
1 GTTATA-TTTGCATGAAATA-TATTAT-TATATATTATGTAATCTATATCGTTATGATCATTGTT
3750039 TTCTATG
63 TTCTATG
*
3750046 GTTATATCTGCATGAAAT
1 GTTATATTTGCATGAAAT
3750064 GATGATGCAT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
66 6 0.08
67 7 0.09
68 3 0.04
69 1 0.01
70 5 0.06
71 48 0.62
72 7 0.09
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (69 bp):
GTTATATTTGCATGAAATATATTATTATATATTATGTAATCTATATCGTTATGATCATTGTTTTC
TATG
Found at i:3753958 original size:16 final size:15
Alignment explanation
Indices: 3753937--3753966 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3753927 AAAATGTCAG
3753937 CTTTTCGGCATTTTGA
1 CTTTTCGGC-TTTTGA
3753953 CTTTTCGGCTTTTG
1 CTTTTCGGCTTTTG
3753967 CCGATCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.07, C:0.20, G:0.20, T:0.53
Consensus pattern (15 bp):
CTTTTCGGCTTTTGA
Found at i:3762915 original size:5 final size:5
Alignment explanation
Indices: 3762905--3762942 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
3762895 TTTGTGTGTT
3762905 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
3762943 TCACAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:3762930 original size:14 final size:14
Alignment explanation
Indices: 3762905--3762941 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3762895 TTTGTGTGTT
3762905 TTTTATTTTATTTTA
1 TTTTA-TTTATTTTA
3762920 TTTTATTTATTTTA
1 TTTTATTTATTTTA
3762934 TTTTATTT
1 TTTTATTT
3762942 TTCACAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:3762930 original size:19 final size:19
Alignment explanation
Indices: 3762906--3762942 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3762896 TTGTGTGTTT
3762906 TTTATTTTATTTTATTTTA
1 TTTATTTTATTTTATTTTA
3762925 TTTATTTTATTTTATTTT
1 TTTATTTTATTTTATTTT
3762943 TCACAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTATTTTATTTTATTTTA
Found at i:3767299 original size:5 final size:5
Alignment explanation
Indices: 3767289--3767320 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3767279 TTGTGTGTTC
3767289 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3767321 TCACATCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:3767303 original size:9 final size:9
Alignment explanation
Indices: 3767289--3767319 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3767279 TTGTGTGTTC
3767289 TTTATTTTA
1 TTTATTTTA
3767298 TTTATTTTA
1 TTTATTTTA
3767307 TTTTATTTTA
1 -TTTATTTTA
3767317 TTT
1 TTT
3767320 TTCACATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:3774656 original size:17 final size:19
Alignment explanation
Indices: 3774634--3774676 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3774624 ATGGAAATAT
3774634 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGC
*
3774651 AATCTTAGATATGATATGC
1 AATCTTACATATGATATGC
3774670 AATCTTA
1 AATCTTA
3774677 GAAGATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 16 0.70
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCTTACATATGATATGC
Found at i:3774687 original size:22 final size:19
Alignment explanation
Indices: 3774642--3774678 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3774632 ATAATCTTCA
3774642 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
3774661 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
3774679 AGATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:3775718 original size:20 final size:21
Alignment explanation
Indices: 3775678--3775728 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
3775668 TAGACATATA
3775678 AATACATATAAAAAACAAATGT
1 AATA-ATATAAAAAACAAATGT
*
3775700 AATAATATAAAAAA-TAATGT
1 AATAATATAAAAAACAAATGT
*
3775720 AGTAATATA
1 AATAATATA
3775729 TATATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 13 0.48
21 10 0.37
22 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (21 bp):
AATAATATAAAAAACAAATGT
Found at i:3789690 original size:23 final size:22
Alignment explanation
Indices: 3789640--3789702 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
3789630 TAGACATATA
*
3789640 AATACATATAAAA-AACAAATGT
1 AATA-ATATAAAATAAAAAATGT
3789662 AATAATATAAAATAAAATAATGT
1 AATAATATAAAATAAAA-AATGT
* *
3789685 AGTAATATATATATAAAA
1 AATAATATA-AAATAAAA
3789703 CAAAAAACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.23
22 7 0.20
23 13 0.37
24 7 0.20
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (22 bp):
AATAATATAAAATAAAAAATGT
Found at i:3838451 original size:40 final size:39
Alignment explanation
Indices: 3838361--3838544 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
3838351 TTGAATGATG
* * *
3838361 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
3838400 ATCCAGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAT
* *
3838441 TCCGGGCTAAGACCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
*
3838480 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAT
* *
3838519 AACCGGGCTATGTCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCGAAGGCATTTG
3838545 AATGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
39 49 0.40
40 63 0.52
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:3838461 original size:39 final size:39
Alignment explanation
Indices: 3838407--3838544 Score: 179
Period size: 39 Copynumber: 3.5 Consensus size: 39
3838397 CATATCCAGA
*
3838407 CTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGG
1 CTAAGA-CCGAAGGCATTTGTGCGAGTTACTAATTCCGGG
*
3838447 CTAAGACCGAAGGCATTTGTGCGAGTTACTAAATCCGGG
1 CTAAGACCGAAGGCATTTGTGCGAGTTACTAATTCCGGG
* * *
3838486 TTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGG
1 CTAAG-ACCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGG
* *
3838526 CTATGTCCGAAGGCATTTG
1 CTAAGACCGAAGGCATTTG
3838545 AATGAGTAGC
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 49 0.56
40 38 0.44
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (39 bp):
CTAAGACCGAAGGCATTTGTGCGAGTTACTAATTCCGGG
Found at i:3838562 original size:79 final size:78
Alignment explanation
Indices: 3838414--3838577 Score: 197
Period size: 79 Copynumber: 2.1 Consensus size: 78
3838404 AGACTAAGAT
* **
3838414 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGACCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGACCGAAGGCATTTGAACGAGTTACTAA
*
3838479 ATCCGGGTTAAGTC
66 ATCC-GGTTAAATC
* * * *
3838493 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCGAAGGCATTTGAATGAG-TAGCT
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAGACCGAAGGCATTTGAACGAGTTA-CT
* *
3838556 ATATCCGGTTAAATT
64 AAATCCGGTTAAATC
3838571 CCGAAGG
1 CCGAAGG
3838578 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
78 18 0.25
79 55 0.75
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGACCGAAGGCATTTGAACGAGTTACTAA
ATCCGGTTAAATC
Found at i:3853389 original size:6 final size:6
Alignment explanation
Indices: 3853380--3853445 Score: 80
Period size: 6 Copynumber: 11.0 Consensus size: 6
3853370 GATGATGATG
* *
3853380 TTTAAT TTTA-T TTTATT TTTATT TTTATT TTTATT TTCATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* *
3853427 TTCATT TTATGTT TTTATT
1 TTTATT TT-TATT TTTATT
3853446 AGTTTCACAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
5 5 0.10
6 43 0.83
7 4 0.08
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:3855014 original size:112 final size:112
Alignment explanation
Indices: 3854817--3855043 Score: 445
Period size: 112 Copynumber: 2.0 Consensus size: 112
3854807 GAGTGCTTCA
3854817 TTTATTGTCCTTAAACACCTCGAGTGATTTGAGTGAATCTTTAGTAAGGATGTGAAACTCTGTGA
1 TTTATTGTCCTTAAACACCTCGAGTGATTTGAGTGAATCTTTAGTAAGGATGTGAAACTCTGTGA
3854882 CATTTCGAATCAAAGGTAATTACTTAAACAAGGGGAGACACCTATGT
66 CATTTCGAATCAAAGGTAATTACTTAAACAAGGGGAGACACCTATGT
3854929 TTTATTGTCCTTAAACACCTCGAGTGATTTGAGTGAATCTTTAGTAAGGATGTGAAACTCTGTGA
1 TTTATTGTCCTTAAACACCTCGAGTGATTTGAGTGAATCTTTAGTAAGGATGTGAAACTCTGTGA
*
3854994 CATTTTGAATCAAAGGTAATTACTTAAACAAGGGGAGACACCTATGT
66 CATTTCGAATCAAAGGTAATTACTTAAACAAGGGGAGACACCTATGT
3855041 TTT
1 TTT
3855044 CTTGATAAAA
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 114 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (112 bp):
TTTATTGTCCTTAAACACCTCGAGTGATTTGAGTGAATCTTTAGTAAGGATGTGAAACTCTGTGA
CATTTCGAATCAAAGGTAATTACTTAAACAAGGGGAGACACCTATGT
Found at i:3859453 original size:14 final size:14
Alignment explanation
Indices: 3859434--3859460 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3859424 TATCAAAACG
3859434 ATAATTAAGAACAC
1 ATAATTAAGAACAC
3859448 ATAATTAAGAACA
1 ATAATTAAGAACA
3859461 AGTCAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
ATAATTAAGAACAC
Found at i:3859836 original size:13 final size:13
Alignment explanation
Indices: 3859818--3859843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3859808 GTTCGGTTGG
3859818 GACACGCCCGTGT
1 GACACGCCCGTGT
3859831 GACACGCCCGTGT
1 GACACGCCCGTGT
3859844 ACAATTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:3862516 original size:39 final size:39
Alignment explanation
Indices: 3862468--3862568 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
3862458 AGCTCGATGA
* *
3862468 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
* *
3862507 GCTTTAGTTAGCCTTCAGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
* *
3862546 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
3862569 AAATCACGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
Found at i:3862550 original size:21 final size:21
Alignment explanation
Indices: 3862486--3862550 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 21
3862476 TAGCCTTCGG
* *
3862486 GCTTCCGTTTAGCACTTGTGT
1 GCTTCCATTTAGCACTTATGT
* *
3862507 GCTT-TAGTTAGC-CTTCA-G-
1 GCTTCCATTTAGCACTT-ATGT
3862525 GCTTCCATTTAGCACTTATGT
1 GCTTCCATTTAGCACTTATGT
3862546 GCTTC
1 GCTTC
3862551 AGCTAGACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
18 4 0.12
19 11 0.33
20 9 0.27
21 9 0.27
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.42
Consensus pattern (21 bp):
GCTTCCATTTAGCACTTATGT
Found at i:3863260 original size:3 final size:3
Alignment explanation
Indices: 3863254--3863282 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3863244 GTTTTTTTTT
3863254 TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3863283 ATTTCGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3865697 original size:21 final size:21
Alignment explanation
Indices: 3865671--3865710 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3865661 GACTTCTCAA
*
3865671 TCAATCAGACAGTCAAATATT
1 TCAATCAAACAGTCAAATATT
*
3865692 TCAATCAAATAGTCAAATA
1 TCAATCAAACAGTCAAATA
3865711 GATACTGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.28
Consensus pattern (21 bp):
TCAATCAAACAGTCAAATATT
Found at i:3866360 original size:14 final size:14
Alignment explanation
Indices: 3866341--3866380 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3866331 CTAAAAGCTT
3866341 TGTATGCAGATGTA
1 TGTATGCAGATGTA
* *
3866355 TGTATGCAAACGTA
1 TGTATGCAGATGTA
*
3866369 TGTATGCGGATG
1 TGTATGCAGATG
3866381 CCCCAACACA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.33
Consensus pattern (14 bp):
TGTATGCAGATGTA
Found at i:3870176 original size:18 final size:18
Alignment explanation
Indices: 3870153--3870201 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
3870143 ATGTGAGGTA
*
3870153 AGTATTAATATTAGTATT
1 AGTATTATTATTAGTATT
3870171 AGTATTATTATTAGTATT
1 AGTATTATTATTAGTATT
*
3870189 ATTATTATTATTA
1 AGTATTATTATTA
3870202 TGAGTGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (18 bp):
AGTATTATTATTAGTATT
Found at i:3870181 original size:3 final size:3
Alignment explanation
Indices: 3870155--3870202 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
3870145 GTGAGGTAAG
* * * *
3870155 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3870203 GAGTGGGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:3870202 original size:12 final size:12
Alignment explanation
Indices: 3870155--3870202 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
3870145 GTGAGGTAAG
* *
3870155 TATTAATATTAG
1 TATTAGTATTAT
3870167 TATTAGTATTAT
1 TATTAGTATTAT
3870179 TATTAGTATTAT
1 TATTAGTATTAT
*
3870191 TATTATTATTAT
1 TATTAGTATTAT
3870203 GAGTGGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:3870397 original size:24 final size:22
Alignment explanation
Indices: 3870343--3870400 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
3870333 TGTGTGAAGT
*
3870343 TGTGAAATAATTATTGATTGAAA
1 TGTGAAA-AATGATTGATTGAAA
*
3870366 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTG-ATTG-AAA
3870391 TGTGAAAAAT
1 TGTGAAAAAT
3870401 TTGTAATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 9 0.31
24 15 0.52
25 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (22 bp):
TGTGAAAAATGATTGATTGAAA
Found at i:3870618 original size:37 final size:39
Alignment explanation
Indices: 3870559--3870654 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
3870549 CGGATAGATT
* * * *
3870559 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
3870596 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
3870635 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
3870655 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:3873070 original size:50 final size:49
Alignment explanation
Indices: 3872961--3873090 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 49
3872951 TCTGGTAGCA
* * ** *
3872961 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
* * *
3873010 TAGTAGCCTGCATTTAGTATTACACACGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACG
3873060 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
3873091 TTACAGTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 27 0.39
50 38 0.55
51 4 0.06
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
Found at i:3876301 original size:24 final size:25
Alignment explanation
Indices: 3876255--3876301 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3876245 CTATAGAGAA
*
3876255 CTAATTTGATTATCTTTTTGTACAT
1 CTAATTTGATTATCTTTTAGTACAT
*
3876280 CTAATTTGATTGT-TTTTAGTAC
1 CTAATTTGATTATCTTTTAGTAC
3876302 TTATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (25 bp):
CTAATTTGATTATCTTTTAGTACAT
Found at i:3879989 original size:27 final size:27
Alignment explanation
Indices: 3879944--3880018 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
3879934 AGGGTAATTT
3879944 TTTTTAATATGAATATTAATATAAAAATA
1 TTTTTAAT-T-AATATTAATATAAAAATA
3879973 TTTTTAATTAATATTAATATAAAAATA
1 TTTTTAATTAATATTAATATAAAAATA
* *
3880000 TTTTAAATTTAATTTTAAT
1 TTTTTAA-TTAATATTAAT
3880019 GAGGTGGTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 24 0.56
28 11 0.26
29 8 0.19
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TTTTTAATTAATATTAATATAAAAATA
Found at i:3891924 original size:16 final size:17
Alignment explanation
Indices: 3891903--3891941 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3891893 TTGGAATTTA
*
3891903 TTTTATGTATTT-TTCT
1 TTTTATGAATTTATTCT
*
3891919 TTTTATGAATTTATTTT
1 TTTTATGAATTTATTCT
3891936 TTTTAT
1 TTTTAT
3891942 TGTTTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTATGAATTTATTCT
Found at i:3891968 original size:20 final size:21
Alignment explanation
Indices: 3891943--3891981 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3891933 TTTTTTTATT
3891943 GTTTAAATT-TTAA-ATTTTAA
1 GTTT-AATTATTAATATTTTAA
3891963 GTTTAATTATTAATATTTT
1 GTTTAATTATTAATATTTT
3891982 TAAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
GTTTAATTATTAATATTTTAA
Found at i:3892559 original size:21 final size:24
Alignment explanation
Indices: 3892535--3892583 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 24
3892525 AATTTTCTTG
*
3892535 TTTTATT-TTAAAA-TTTAATT-A
1 TTTTATTGTGAAAATTTTAATTAA
3892556 TTTT-TTGTGAAAATTTTAATTAA
1 TTTTATTGTGAAAATTTTAATTAA
3892579 TTTTA
1 TTTTA
3892584 AACATTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 2 0.09
21 9 0.39
22 7 0.30
23 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTTATTGTGAAAATTTTAATTAA
Found at i:3899851 original size:30 final size:29
Alignment explanation
Indices: 3899815--3899879 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 29
3899805 AAACGGAAGT
3899815 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTT-AACTAGC
3899845 TTTGGCACTAAGTGTGCGATTTAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAACTAGC
3899874 TTTGGC
1 TTTGGC
3899880 TACTTGAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 13 0.37
30 22 0.63
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGCGATTTAACTAGC
Found at i:3907299 original size:25 final size:25
Alignment explanation
Indices: 3907265--3907314 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3907255 CGATACCGAC
3907265 TTAGTCTCGGTTATTTGAGATGGCA
1 TTAGTCTCGGTTATTTGAGATGGCA
3907290 TTAGTCTCGGTTATTTGAGATGGCA
1 TTAGTCTCGGTTATTTGAGATGGCA
3907315 CTAAGTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (25 bp):
TTAGTCTCGGTTATTTGAGATGGCA
Found at i:3910782 original size:20 final size:20
Alignment explanation
Indices: 3910731--3910784 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
3910721 GACATTGAAC
* * *
3910731 TTAAATAACTTATATTTATT
1 TTAAATAATTTAAATATATT
*
3910751 TTATAA-ATTTTAAATATATT
1 TTA-AATAATTTAAATATATT
3910771 TTAAATAATTTAAA
1 TTAAATAATTTAAA
3910785 GAATATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAAATAATTTAAATATATT
Found at i:3914356 original size:19 final size:18
Alignment explanation
Indices: 3914324--3914359 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3914314 ATTTGCAATA
3914324 ATATTTTTTAATTTTTAT
1 ATATTTTTTAATTTTTAT
*
3914342 ATATTATTTTTATTTTTA
1 ATATT-TTTTAATTTTTA
3914360 AAATTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
ATATTTTTTAATTTTTAT
Found at i:3914537 original size:21 final size:22
Alignment explanation
Indices: 3914511--3914551 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3914501 GGCTATGTGG
*
3914511 TCGCTCAAC-ATTGGTCAACCC
1 TCGCTCAACGACTGGTCAACCC
3914532 TCGCTCAACGACTGGTCAAC
1 TCGCTCAACGACTGGTCAAC
3914552 AATCGGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.22
Consensus pattern (22 bp):
TCGCTCAACGACTGGTCAACCC
Found at i:3915150 original size:40 final size:40
Alignment explanation
Indices: 3915106--3915182 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
3915096 TTAATAATGG
*
3915106 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
1 GTTAGGTAAATGTTCCATGATAATGGATTAAGTAAATATT
*
3915146 GTTAGGTAAATGTTCCATGATAATGGTTTAAGTAAAT
1 GTTAGGTAAATGTTCCATGATAATGGATTAAGTAAAT
3915183 GTTCCATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (40 bp):
GTTAGGTAAATGTTCCATGATAATGGATTAAGTAAATATT
Found at i:3916734 original size:26 final size:25
Alignment explanation
Indices: 3916682--3916734 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
3916672 TTTACAGTTT
3916682 TACCCCTAGTAGATAAATTACCGAAA
1 TACCCCTAG-AGATAAATTACCGAAA
*
3916708 TACCCCTAG-GATTAAATTGACCTAAA
1 TACCCCTAGAGA-TAAATT-ACCGAAA
3916734 T
1 T
3916735 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.08
25 6 0.25
26 16 0.67
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (25 bp):
TACCCCTAGAGATAAATTACCGAAA
Found at i:3922117 original size:40 final size:40
Alignment explanation
Indices: 3922073--3922149 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
3922063 TTGATAATGG
3922073 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
1 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
*
3922113 GTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAAT
1 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAAT
3922150 GTTCCATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (40 bp):
GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
Found at i:3932686 original size:26 final size:26
Alignment explanation
Indices: 3932655--3932738 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 26
3932645 GACACCTTAA
*
3932655 AAATAACATACAAAAGAGTTTAAAAT
1 AAATAATATACAAAAGAGTTTAAAAT
**
3932681 AAATAATATGTAAAAGAGAAATTTAAAAT
1 AAATAATATACAAAAGAG---TTTAAAAT
* *
3932710 AAATAATGTACAAAAACAGTTT-AAAT
1 AAATAATATAC-AAAAGAGTTTAAAAT
3932736 AAA
1 AAA
3932739 AAATTATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 22 0.47
27 3 0.06
29 16 0.34
30 6 0.13
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (26 bp):
AAATAATATACAAAAGAGTTTAAAAT
Found at i:3933478 original size:27 final size:27
Alignment explanation
Indices: 3933368--3933499 Score: 83
Period size: 27 Copynumber: 5.0 Consensus size: 27
3933358 TAAAAAAAAC
* * * * *
3933368 TTAAAATAGATAATACATATATAATGGT
1 TTAAAATAAATAATATATGTAAAAT-AT
** *
3933396 TTAAAATAAATAACGTAT-AAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
* * * *
3933422 TTCAAAATAAGT-A-ATATGTACAGTAG
1 TT-AAAATAAATAATATATGTAAAATAT
3933448 TTAAAATAAATAATATATGTAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
** *
3933475 TTAAAATTTATAATA-ATTTAAAATA
1 TTAAAATAAATAATATATGTAAAATA
3933500 CATAAGACGT
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
25 11 0.14
26 20 0.25
27 35 0.44
28 14 0.17
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (27 bp):
TTAAAATAAATAATATATGTAAAATAT
Found at i:3933573 original size:25 final size:26
Alignment explanation
Indices: 3933520--3933585 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
3933510 AAAAAAAGGA
* * *
3933520 TTAAAATAAGTAATA-ATAAAATTAT
1 TTAAAATAAATAATATATAAAATAAC
3933545 TTAAAATAAATAATATATAAAA-AAC
1 TTAAAATAAATAATATATAAAATAAC
3933570 TTAAAA-AGAATAATAT
1 TTAAAATA-AATAATAT
3933586 TAACAGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 29 0.81
26 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:3942185 original size:15 final size:16
Alignment explanation
Indices: 3942167--3942209 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
3942157 AAACTTAAAA
3942167 AAAAAAAAACACA-CT
1 AAAAAAAAACACACCT
*
3942182 AAAAAAAAAAACACCT
1 AAAAAAAAACACACCT
* *
3942198 ACAAACAAACAC
1 AAAAAAAAACAC
3942210 CAAAAACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.72, C:0.23, G:0.00, T:0.05
Consensus pattern (16 bp):
AAAAAAAAACACACCT
Found at i:3942440 original size:20 final size:22
Alignment explanation
Indices: 3942417--3942475 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
3942407 TAAAAAAAAA
*
3942417 AAAAAAAAACAAACAC-CA-CT
1 AAAAAAAAACAAACACTAACCT
3942437 AAAACAAAACACCAAACACTAACCT
1 AAAA-AAAA-A-CAAACACTAACCT
3942462 AAAGAAAAAACAAA
1 AAA-AAAAAACAAA
3942476 AAACAAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
20 4 0.12
21 4 0.12
22 1 0.03
23 11 0.34
24 2 0.06
25 9 0.28
26 1 0.03
ACGTcount: A:0.69, C:0.24, G:0.02, T:0.05
Consensus pattern (22 bp):
AAAAAAAAACAAACACTAACCT
Found at i:3942475 original size:23 final size:20
Alignment explanation
Indices: 3942417--3942645 Score: 78
Period size: 19 Copynumber: 11.4 Consensus size: 20
3942407 TAAAAAAAAA
*
3942417 AAAAAAAAACAAACACCACT
1 AAAAAAAAACAAACACAACT
3942437 AAAACAAAACACCAAACACTAACCT
1 AAAA-AAAA-A-CAAACAC-AA-CT
3942462 AAAGAAAAAACAAA-A-AAC-
1 AAA-AAAAAACAAACACAACT
*
3942480 AAAAACACAACAAA-ACTAA--
1 AAAAA-AAAACAAACAC-AACT
* * * **
3942499 AAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAACAAACACAACT
*
3942519 AAAAACAAAACTAAA-ACAACA
1 AAAAA-AAAAC-AAACACAACT
3942540 AAACAAAACTAACAAA-ACAAACT
1 AAA-AAAA--AACAAACAC-AACT
*
3942563 AAAATAAAACAAA-A-AA-T
1 AAAAAAAAACAAACACAACT
*
3942580 AAAAAAAAA-AAA-AAAACT
1 AAAAAAAAACAAACACAACT
*
3942598 -AAAAAAAACTAAA-AAAACT
1 AAAAAAAAAC-AAACACAACT
*
3942617 -AAAAAAAACATAACTA-ATCT
1 AAAAAAAAACA-AAC-ACAACT
3942637 AAAAAAAAA
1 AAAAAAAAA
3942646 AAAAATAAAA
Statistics
Matches: 171, Mismatches: 12, Indels: 51
0.73 0.05 0.22
Matches are distributed among these distances:
16 4 0.02
17 21 0.12
18 23 0.13
19 27 0.16
20 23 0.13
21 26 0.15
22 15 0.09
23 20 0.12
24 2 0.01
25 9 0.05
26 1 0.01
ACGTcount: A:0.77, C:0.15, G:0.00, T:0.07
Consensus pattern (20 bp):
AAAAAAAAACAAACACAACT
Found at i:3942476 original size:5 final size:5
Alignment explanation
Indices: 3942475--3942626 Score: 83
Period size: 5 Copynumber: 31.2 Consensus size: 5
3942465 GAAAAAACAA
* * * *
3942475 AAAAC AAAAAC ACAAC AAAAC TAAAA- AAAA- AAAAA AAAAA AAAAA AAAAC
1 AAAAC -AAAAC AAAAC AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
* *
3942525 AAAAC TAAAAC --AAC AAAAC AAAAC -TAAC AAAAC -AAAC TAAAAT AAAAC
1 AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC -AAAAC AAAAC
* * *
3942573 AAAA- AATAA- AAAAA AAAAA AAAAC TAAAA- AAAAC TAAA- AAAAC TAAAA-
1 AAAAC AA-AAC AAAAC AAAAC AAAAC -AAAAC AAAAC AAAAC AAAAC -AAAAC
3942621 AAAAC A
1 AAAAC A
3942627 TAACTAATCT
Statistics
Matches: 121, Mismatches: 10, Indels: 31
0.75 0.06 0.19
Matches are distributed among these distances:
3 3 0.02
4 30 0.25
5 63 0.52
6 25 0.21
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (5 bp):
AAAAC
Found at i:3942535 original size:89 final size:84
Alignment explanation
Indices: 3942327--3942658 Score: 229
Period size: 89 Copynumber: 3.9 Consensus size: 84
3942317 CTACAACAAC
** * * * *
3942327 AAAAAAAAAAAAACTAACAAAAAATACAAAACTAAAA-AACATAAACAAACCTAA-AGAA-AAA-
1 AAAAAAAAAAAAAAAAAAAAAAAAAACAAAACTAAAACAACA-AAACAAAACTAACAAAACAAAC
* ** *
3942388 AAAGACTAAATAAATAAACTA
65 AAAAAAAAAACAAA-AAACTA
* * ** * * *
3942409 AAAAAAAAAAAAAAAAACAAACACCACTAAAAC-AAAACACCAAACACTAACCTAA-AGAAA-AA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAC-AAAACTAAAACAACAAA-ACAAAACTAACA-AAACAA
3942471 ACAAAAAACAAAAACACAACAAAACTA
63 AC--AAAA-AAAAA-ACAA-AAAACTA
*
3942498 AAAAAAAAAAAAAAAAAAAAAAAAAACAAAACTAAAACAACAAAACAAAACTAACAAAACAAACT
1 AAAAAAAAAAAAAAAAAAAAAAAAAACAAAACTAAAACAACAAAACAAAACTAACAAAACAAACA
*
3942563 AAAATAAAACAAAAAA-TA
66 AAAAAAAAACAAAAAACTA
* * * *
3942581 AAAAAAAAAAAAAAACTAAAAAAAACTAAA-AAAACTAAAAAAAACATAACTAATCTAA-AAAA-
1 AAAAAAAAAAAAAAA--AAAAAAAA--AAACAAAACT-AAAACAACAAAACAAAACTAACAAAAC
3942643 AAA-AAAAATAAAAACA
61 AAACAAAAA-AAAAACA
3942659 TCCTAAAAAA
Statistics
Matches: 204, Mismatches: 27, Indels: 35
0.77 0.10 0.13
Matches are distributed among these distances:
82 28 0.14
83 35 0.17
84 13 0.06
85 21 0.10
86 14 0.07
87 26 0.13
88 19 0.09
89 47 0.23
90 1 0.00
ACGTcount: A:0.77, C:0.14, G:0.01, T:0.08
Consensus pattern (84 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAACAAAACTAAAACAACAAAACAAAACTAACAAAACAAACA
AAAAAAAAACAAAAAACTA
Found at i:3942578 original size:94 final size:90
Alignment explanation
Indices: 3942408--3942626 Score: 211
Period size: 94 Copynumber: 2.4 Consensus size: 90
3942398 TAAATAAACT
* ** * * *
3942408 AAAAAAAAAAAAAAAAAACAAACACCACTAAAACAAAACACCAAACACTAACCTAAAGAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAACAAAACTAAAACAAAACAACAAACACTAACCAAAACAAAAAAC
3942473 AAAAAACAAAAACACAACAAAACTAAAAA
66 AAAAAACAAAAACA-AA-AAAA--AAAAA
3942502 AAAAAAAAAAAAAAAAAAAAAACAAAACTAAAACAACAA-AACAAA-ACTAA-CAAAACAAACTA
1 AAAAAAAAAAAAAAAAAAAAAACAAAACTAAAACAA-AACAACAAACACTAACCAAAACAAA--A
* *
3942564 AA-ATAAAAC-AAAA-AATAAAAAAAAA
63 AACAAAAAACAAAAACAAAAAAAAAAAA
** **
3942589 AAAAAAACTAAAAAAAACTAAA-AAAACTAAAA-AAAACA
1 AAAAAAAAAAAAAAAAAAAAAACAAAACTAAAACAAAACA
3942627 TAACTAATCT
Statistics
Matches: 109, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
84 2 0.02
85 3 0.03
86 10 0.09
87 23 0.21
89 4 0.04
90 1 0.01
91 1 0.01
92 11 0.10
93 11 0.10
94 41 0.38
95 2 0.02
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.05
Consensus pattern (90 bp):
AAAAAAAAAAAAAAAAAAAAAACAAAACTAAAACAAAACAACAAACACTAACCAAAACAAAAAAC
AAAAAACAAAAACAAAAAAAAAAAA
Found at i:3942602 original size:83 final size:83
Alignment explanation
Indices: 3942327--3942620 Score: 223
Period size: 83 Copynumber: 3.4 Consensus size: 83
3942317 CTACAACAAC
* * *
3942327 AAAAAAAAAAAAACTAACAAAAAATACAAAACTAAAA-AACATAAACAAACCTAAAGAAAAAAAA
1 AAAAAAAAAAAAACTAA-AAAAAACACAAAACTAAAACAACA-AAACAAAACT--A-ACAAAAAA
*
3942391 GACTAAATAAATAAACTAAAAAAAAAA
61 -ACTAAA-AAA-AAAC-AAAAAATAAA
* *
3942418 AAAAAAAACAAACACCACTAAAACAAAACACCAAACACT--AAC--CTAAAGAAAA--AAC-AAA
1 AAAAAAAA-AAA-A--ACTAAAA-AAAACA-CAAA-ACTAAAACAACAAAACAAAACTAACAAAA
* *
3942476 AAAC-AAAAACACAAC-AAAACTAAA
59 AAACTAAAAA-AAAACAAAAAATAAA
* *
3942500 AAAAAAAAAAAAA-AAAAAAAAAAACAAAACTAAAACAACAAAACAAAACTAACAAAACAAACTA
1 AAAAAAAAAAAAACTAAAAAAAACACAAAACTAAAACAACAAAACAAAACTAACAAAA-AAACTA
*
3942564 AAATAAAACAAAAAATAAA
65 AAAAAAAACAAAAAATAAA
*
3942583 AAAAAAAAAAAAACTAAAAAAAACTAAAAAAACTAAAA
1 AAAAAAAAAAAAACTAAAAAAAAC--ACAAAACTAAAA
3942621 AAAACATAAC
Statistics
Matches: 163, Mismatches: 18, Indels: 49
0.71 0.08 0.21
Matches are distributed among these distances:
74 3 0.02
75 4 0.02
76 8 0.05
77 4 0.02
78 9 0.06
80 4 0.02
81 6 0.04
82 23 0.14
83 25 0.15
84 13 0.08
85 4 0.02
86 13 0.08
87 5 0.03
88 1 0.01
89 1 0.01
91 8 0.05
92 3 0.02
93 7 0.04
94 3 0.02
95 12 0.07
96 4 0.02
97 3 0.02
ACGTcount: A:0.78, C:0.14, G:0.01, T:0.07
Consensus pattern (83 bp):
AAAAAAAAAAAAACTAAAAAAAACACAAAACTAAAACAACAAAACAAAACTAACAAAAAAACTAA
AAAAAAACAAAAAATAAA
Found at i:3942644 original size:1 final size:1
Alignment explanation
Indices: 3942497--3942624 Score: 67
Period size: 1 Copynumber: 128.0 Consensus size: 1
3942487 CAACAAAACT
* ** * * * ** * * *
3942497 AAAAAAAAAAAAAAAAAAAAAAAAAAACAAAACTAAAACAACAAAACAAAACTAACAAAACAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * ** ** **
3942562 TAAAATAAAACAAAAAATAAAAAAAAAAAAAAAACTAAAAAAAACTAAAAAAACTAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3942625 CATAACTAAT
Statistics
Matches: 91, Mismatches: 36, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 91 1.00
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:3942655 original size:9 final size:9
Alignment explanation
Indices: 3942491--3942656 Score: 85
Period size: 9 Copynumber: 18.2 Consensus size: 9
3942481 AAAACACAAC
*
3942491 AAAACTAAA
1 AAAAATAAA
3942500 AAAAA-AAA
1 AAAAATAAA
3942508 AAAAA-AAA
1 AAAAATAAA
3942516 AAAAA-AAA
1 AAAAATAAA
*
3942524 CAAAACTAAA
1 -AAAAATAAA
3942534 ACAACAA-AACA
1 A-AA-AATAA-A
*
3942545 AAACTAACAAA
1 AAA--AATAAA
*
3942556 ACAAACTAAA
1 A-AAAATAAA
* *
3942566 ATAAA-ACA
1 AAAAATAAA
3942574 AAAAATAAA
1 AAAAATAAA
3942583 AAAAA-AAA
1 AAAAATAAA
3942591 AAAAACTAAA
1 AAAAA-TAAA
3942601 AAAAACTAAA
1 AAAAA-TAAA
*
3942611 AAAACTAAA
1 AAAAATAAA
* *
3942620 AAAAACATA
1 AAAAATAAA
** **
3942629 ACTAATCTA
1 AAAAATAAA
3942638 AAAAA-AAA
1 AAAAATAAA
3942646 AAAAATAAA
1 AAAAATAAA
3942655 AA
1 AA
3942657 CATCCTAAAA
Statistics
Matches: 122, Mismatches: 23, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
8 39 0.32
9 41 0.34
10 31 0.25
11 7 0.06
12 4 0.03
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAATAAA
Found at i:3942957 original size:18 final size:18
Alignment explanation
Indices: 3942931--3943018 Score: 58
Period size: 17 Copynumber: 4.8 Consensus size: 18
3942921 TAAACAAAAC
*
3942931 ACAACAAAAAAATACTAA
1 ACAAAAAAAAAATACTAA
*
3942949 ACAAAAAAAAAAGAAACCATAA
1 AC-AAAAAAAAA-ATA-C-TAA
3942971 A-AAAAAAAAAACT-CTAA
1 ACAAAAAAAAAA-TACTAA
* *
3942988 ATAAAAAAATAA-AC-AA
1 ACAAAAAAAAAATACTAA
3943004 ACACAAAAAAAAATA
1 ACA-AAAAAAAAATA
3943019 AAAGACAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
16 4 0.07
17 13 0.24
18 13 0.24
19 9 0.16
20 11 0.20
21 1 0.02
22 4 0.07
ACGTcount: A:0.77, C:0.12, G:0.01, T:0.09
Consensus pattern (18 bp):
ACAAAAAAAAAATACTAA
Found at i:3942965 original size:15 final size:14
Alignment explanation
Indices: 3942933--3943421 Score: 118
Period size: 14 Copynumber: 32.8 Consensus size: 14
3942923 AACAAAACAC
**
3942933 AACAAAAAAATACTA
1 AACAAAAAAA-AAAA
3942948 AACAAAAAAAAAAGA
1 AACAAAAAAAAAA-A
3942963 AACCATAAAAAAAAAAA
1 AA-C--AAAAAAAAAAA
3942980 AACTCTAAATAAAAAAATA
1 AA--C-AAA-AAAAAAA-A
3942999 AACAAACACAAAAAAA
1 AACAAA-A-AAAAAAA
* *
3943015 AATAAAAGACAAAAATT
1 AACAAAA-A-AAAAA-A
*
3943032 AA-AAAAACAAAAA
1 AACAAAAAAAAAAA
* * **
3943045 AACACCACAACTAAA
1 AACA-AAAAAAAAAA
* *
3943060 AAGAAAAAAACTAAA
1 AACAAAAAAA-AAAA
3943075 AACATAATAAAAAAAA
1 AACA-AA-AAAAAAAA
* *
3943091 AAC-TAACAAAAAA
1 AACAAAAAAAAAAA
3943104 AA-AAAAAAAAAAA
1 AACAAAAAAAAAAA
*
3943117 AA-ATAAAAAAAAA
1 AACAAAAAAAAAAA
** ***
3943130 AACTTACTTAAAAA
1 AACAAAAAAAAAAA
*** *
3943144 AACTCTAAGAAAAA
1 AACAAAAAAAAAAA
3943158 AACAAAAATATAAAAA
1 AACAAAAA-A-AAAAA
3943174 AA-AAAAAAAAAAA
1 AACAAAAAAAAAAA
**
3943187 AACACCTAAAAAAAA
1 AACA-AAAAAAAAAA
* * *
3943202 AA-AATACACAAAA
1 AACAAAAAAAAAAA
***
3943215 AAC-AAAATCCAAA
1 AACAAAAAAAAAAA
*
3943228 AACTACTAAAAAAAAA
1 AAC-A-AAAAAAAAAA
* * * *
3943244 ACCACAACAATAAA
1 AACAAAAAAAAAAA
3943258 AACAAAAAAACAAAA
1 AACAAAAAAA-AAAA
* *
3943273 AAC--TAAAAATAA
1 AACAAAAAAAAAAA
*
3943285 ACCTAAAAAAAACTAAA
1 AAC-AAAAAAAA--AAA
3943302 AACAAAAAATTATAAAA
1 AACAAAAAA--A-AAAA
3943319 ACTACTAAAAAATAACAAA
1 A--AC-AAAAAA-AA-AAA
3943338 AA-ATAAAAAAAAAA
1 AACA-AAAAAAAAAA
*
3943352 AACAAAAACTTAAATCAA
1 AACAAAAA---AAA-AAA
* *
3943370 AAC-CAAACAAAAA
1 AACAAAAAAAAAAA
3943383 AACAAAAAAAAAAA
1 AACAAAAAAAAAAA
* * **
3943397 AATACAAAAAAAGT
1 AACAAAAAAAAAAA
3943411 AACAAAAAAAA
1 AACAAAAAAAA
3943422 CAAACAAACT
Statistics
Matches: 352, Mismatches: 77, Indels: 91
0.68 0.15 0.17
Matches are distributed among these distances:
12 5 0.01
13 67 0.19
14 86 0.24
15 62 0.18
16 54 0.15
17 35 0.10
18 25 0.07
19 12 0.03
20 6 0.02
ACGTcount: A:0.78, C:0.12, G:0.01, T:0.09
Consensus pattern (14 bp):
AACAAAAAAAAAAA
Found at i:3942972 original size:17 final size:17
Alignment explanation
Indices: 3942951--3943001 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
3942941 AATACTAAAC
3942951 AAAAAAAAAAGAAAC-CAT
1 AAAAAAAAAA-AAACTC-T
3942969 AAAAAAAAAAAAACTCT
1 AAAAAAAAAAAAACTCT
3942986 AAATAAAAAAATAAAC
1 AAA-AAAAAAA-AAAC
3943002 AAACACAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.27
18 18 0.60
19 4 0.13
ACGTcount: A:0.78, C:0.10, G:0.02, T:0.10
Consensus pattern (17 bp):
AAAAAAAAAAAAACTCT
Found at i:3942988 original size:39 final size:40
Alignment explanation
Indices: 3942936--3943021 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
3942926 AAAACACAAC
*
3942936 AAAAAAATACTAAACAAAAAAA-AAAGAAAC-CATAAAAAA
1 AAAAAAATACTAAACAAAAAAATAAACAAACACA-AAAAAA
*
3942975 AAAAAAACT-CTAAATAAAAAAATAAACAAACACAAAAAAA
1 AAAAAAA-TACTAAACAAAAAAATAAACAAACACAAAAAAA
*
3943015 AATAAAA
1 AAAAAAA
3943022 GACAAAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 19 0.46
40 20 0.49
41 2 0.05
ACGTcount: A:0.79, C:0.10, G:0.01, T:0.09
Consensus pattern (40 bp):
AAAAAAATACTAAACAAAAAAATAAACAAACACAAAAAAA
Found at i:3943011 original size:17 final size:15
Alignment explanation
Indices: 3942991--3943407 Score: 109
Period size: 16 Copynumber: 26.4 Consensus size: 15
3942981 ACTCTAAATA
3942991 AAAAAATAAACAAACAC
1 AAAAAATAAA-AAA-AC
*
3943008 AAAAAAAAATAAAAGAC
1 AAAAAATAA-AAAA-AC
*
3943025 AAAAATTAAAAAAAC
1 AAAAAATAAAAAAAC
* *
3943040 AAAAAA-ACACCACAAC
1 AAAAAATA-A-AAAAAC
* *
3943056 TAAAAAGAAAAAAAC
1 AAAAAATAAAAAAAC
3943071 TAAAAACATAATAAAAA-
1 -AAAAA-ATAA-AAAAAC
* *
3943088 AAAAACT-AACAAA-
1 AAAAAATAAAAAAAC
3943101 AAAAAA-AAAAAAA-
1 AAAAAATAAAAAAAC
3943114 AAAAAATAAAAAAA-
1 AAAAAATAAAAAAAC
*
3943128 AAAACTTACTTAAAAAAAC
1 AAAA---A-ATAAAAAAAC
*** *
3943147 -TCTAAGAAAAAAAC
1 AAAAAATAAAAAAAC
3943161 AAAAATATAAAAAAA-
1 AAAAA-ATAAAAAAAC
3943176 AAAAAA-AAAAAAAC
1 AAAAAATAAAAAAAC
*
3943190 ACCTAAAAAAAAAAAATAC
1 A---AAAAATAAAAAA-AC
**
3943209 ACAAAAA-ACAAAATCC
1 A-AAAAATA-AAAAAAC
3943225 AAAAACTACTAAAAAAA-
1 AAAAA--A-TAAAAAAAC
*
3943242 AAACCACAACAATAAAAAC
1 AAA--A-AATAA-AAAAAC
3943261 AAAAAA-ACAAAAAAC
1 AAAAAATA-AAAAAAC
* *
3943276 TAAAAATAAACCTAAA-
1 AAAAAATAAA--AAAAC
*
3943292 AAAAACT--AAAAAC
1 AAAAAATAAAAAAAC
3943305 AAAAAATTATAAAAACTAC
1 AAAAAA-TA-AAAAA--AC
3943324 TAAAAAATAACAAAAA-
1 -AAAAAATAA-AAAAAC
3943340 ATAAAAA-AAAAAAAC
1 A-AAAAATAAAAAAAC
*
3943355 AAAAACTTAAATCAAAAC
1 AAAAA-ATAAA--AAAAC
* *
3943373 --CAAACAAAAAAAC
1 AAAAAATAAAAAAAC
*
3943386 AAAAAAAAAAAAATAC
1 AAAAAATAAAAAA-AC
3943402 AAAAAA
1 AAAAAA
3943408 AGTAACAAAA
Statistics
Matches: 302, Mismatches: 44, Indels: 109
0.66 0.10 0.24
Matches are distributed among these distances:
12 3 0.01
13 37 0.12
14 34 0.11
15 54 0.18
16 61 0.20
17 54 0.18
18 36 0.12
19 16 0.05
20 7 0.02
ACGTcount: A:0.78, C:0.12, G:0.01, T:0.09
Consensus pattern (15 bp):
AAAAAATAAAAAAAC
Found at i:3943116 original size:55 final size:56
Alignment explanation
Indices: 3943056--3943221 Score: 169
Period size: 55 Copynumber: 2.9 Consensus size: 56
3943046 ACACCACAAC
* **
3943056 TAAAAAGAAAAAAACTAAAAACATAATAAAAAAAAAACTAACAAAAAAAAAAAA-A
1 TAAAAAAAAAAAAAAAAAAAACATAATAAAAAAAAAACTAACAAAAAAAAAAAATA
* * * ** *
3943111 -AAAAAAAAATAAAAAAAAAAACTTACTTAAAAAAACTCTAAGAAAAAAACAAAAATA
1 TAAAAAAAAA-AAAAAAAAAAACATAATAAAAAAAAAACTAACAAAAAAA-AAAAATA
*
3943168 TAAAAAAAAAAAAAAAAAAAACACCTAA-AAAAAAAAAA-TACACAAAAAACAAAA
1 TAAAAAAAAAAAAAAAAAAAACA--TAATAAAAAAAAAACTA-ACAAAAAAAAAAA
3943222 TCCAAAAACT
Statistics
Matches: 88, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
54 8 0.09
55 31 0.35
56 5 0.06
57 19 0.22
58 23 0.26
59 2 0.02
ACGTcount: A:0.80, C:0.09, G:0.01, T:0.10
Consensus pattern (56 bp):
TAAAAAAAAAAAAAAAAAAAACATAATAAAAAAAAAACTAACAAAAAAAAAAAATA
Found at i:3943145 original size:1 final size:1
Alignment explanation
Indices: 3943083--3943131 Score: 62
Period size: 1 Copynumber: 49.0 Consensus size: 1
3943073 AAAACATAAT
** * *
3943083 AAAAAAAAAACTAACAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3943132 CTTACTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.92, C:0.04, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:3943186 original size:43 final size:41
Alignment explanation
Indices: 3943139--3943419 Score: 143
Period size: 41 Copynumber: 6.7 Consensus size: 41
3943129 AAACTTACTT
3943139 AAAAAAACTCTAAGAAAAAAACAAAAATATAAAAAAAAAAAAA
1 AAAAAAACTCTAA-AAAAAAACAAAAA-ATAAAAAAAAAAAAA
* * * * *
3943182 AAAAAAACACCTAAAAAAAAA-AAATACA-CAAAAAACAAAAT
1 AAAAAAAC-TCTAAAAAAAAACAAA-AAATAAAAAAAAAAAAA
** * *
3943223 CCAAAAACTACTAAAAAAAAAACCACAACAATAAAAACAAAAAAA
1 AAAAAAACT-CT-AAAAAAAAA-CA-AAAAATAAAAAAAAAAAAA
* *
3943268 CAAAAAA--CTAAAAATAAACCTAAAAAA-AACTAAAAACAAAAAA
1 AAAAAAACTCTAAAAA-AAAAC-AAAAAATAA--AAAAA-AAAAAA
* *
3943311 TTATAAAAACTACTAAAAAATAACAAAAAAT--AAAAAAAAAAA
1 --AAAAAAACT-CTAAAAAAAAACAAAAAATAAAAAAAAAAAAA
* ** * * *
3943353 ACAAAAACT-TAAATCAAAACCAAACA-AAAAAACAAAAAA
1 AAAAAAACTCTAAAAAAAAACAAAAAATAAAAAAAAAAAAA
3943392 AAAAAAA-TAC-AAAAAAAGTAACAAAAAA
1 AAAAAAACT-CTAAAAAAA--AACAAAAAA
3943420 AACAAACAAA
Statistics
Matches: 179, Mismatches: 34, Indels: 52
0.68 0.13 0.20
Matches are distributed among these distances:
38 13 0.07
39 21 0.12
40 10 0.06
41 35 0.20
42 29 0.16
43 27 0.15
44 6 0.03
45 22 0.12
46 6 0.03
47 3 0.02
48 7 0.04
ACGTcount: A:0.77, C:0.13, G:0.01, T:0.09
Consensus pattern (41 bp):
AAAAAAACTCTAAAAAAAAACAAAAAATAAAAAAAAAAAAA
Found at i:3943292 original size:11 final size:10
Alignment explanation
Indices: 3943269--3943303 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
3943259 ACAAAAAAAC
3943269 AAAAAACTAA
1 AAAAAACTAA
3943279 AAATAAACCTAA
1 AAA-AAA-CTAA
3943291 AAAAAACTAA
1 AAAAAACTAA
3943301 AAA
1 AAA
3943304 CAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.43
11 6 0.26
12 7 0.30
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAACTAA
Found at i:3943340 original size:12 final size:12
Alignment explanation
Indices: 3943325--3943421 Score: 52
Period size: 11 Copynumber: 8.5 Consensus size: 12
3943315 AAAAACTACT
3943325 AAAAAATAAC--
1 AAAAAATAACAA
3943335 AAAAAATAA-AA
1 AAAAAATAACAA
3943346 AAAAAA-AACAA
1 AAAAAATAACAA
3943357 AAACTTAAAT--CAA
1 AAA---AAATAACAA
* *
3943370 AACCAAACAA-AA
1 AA-AAAATAACAA
3943382 AAACAAA-AA-AA
1 AAA-AAATAACAA
3943393 AAAAAAT-ACAA
1 AAAAAATAACAA
*
3943404 AAAAAGTAACAA
1 AAAAAATAACAA
3943416 AAAAAA
1 AAAAAA
3943422 CAAACAAACT
Statistics
Matches: 68, Mismatches: 5, Indels: 26
0.69 0.05 0.26
Matches are distributed among these distances:
10 15 0.22
11 29 0.43
12 16 0.24
13 5 0.07
14 3 0.04
ACGTcount: A:0.81, C:0.10, G:0.01, T:0.07
Consensus pattern (12 bp):
AAAAAATAACAA
Found at i:3943395 original size:86 final size:83
Alignment explanation
Indices: 3943063--3943396 Score: 249
Period size: 89 Copynumber: 3.8 Consensus size: 83
3943053 AACTAAAAAG
** *
3943063 AAAAAAACTAAAAACATAATAAAAAAAAAACTAACAAA--AAA-AAAAAAAAAAAAAAAATAAAA
1 AAAAAAAC-AAAAA-ATAA-AAAAAAAAAAC-AA-AAACTAAACAAAACCAAAAAAAAAACAAAA
3943125 AAAAAAACTTACTTAAAAAAACT-CTAA
61 AAAAAAA-TTA--T--AAAAACTACTAA
3943152 GAAAAAAACAAAAATATAAAAAAAAAAAA-AAAAA--AAACACCTAAA--AAAAAAAAATACACA
1 -AAAAAAACAAAAA-ATAAAAAAAAAAAACAAAAACTAAACA---AAACCAAAAAAAAA-ACA-A
**
3943212 AAAAACAAAA-TCCAAAAACTACTAAA
59 AAAAA-AAAATTATAAAAACTACT-AA
* * *
3943238 AAAAAAACCACAACAATAAAAACAAAAAAACAAAAAACTAAAAATAAACC-TAAAAAAAACTAAA
1 AAAAAAA-CA-AAAAATAAAAA-AAAAAAAC-AAAAACTAAACA-AAACCAAAAAAAAAAC-AAA
3943302 AACAAAAAATTATAAAAACTACTAA
60 AA-AAAAAATTATAAAAACTACTAA
*
3943327 AAAATAACAAAAAATAAAAAAAAAAAACAAAAACTTAAATCAAAACCAAACAAAAAAACAAAAAA
1 AAAAAAACAAAAAATAAAAAAAAAAAACAAAAAC-TAAA-CAAAACCAAA-AAAAAAACAAAAAA
3943392 AAAAA
63 AAAAA
3943397 AATACAAAAA
Statistics
Matches: 206, Mismatches: 13, Indels: 54
0.75 0.05 0.20
Matches are distributed among these distances:
84 7 0.03
85 21 0.10
86 37 0.18
87 36 0.17
88 23 0.11
89 45 0.22
90 33 0.16
91 4 0.02
ACGTcount: A:0.78, C:0.12, G:0.00, T:0.10
Consensus pattern (83 bp):
AAAAAAACAAAAAATAAAAAAAAAAAACAAAAACTAAACAAAACCAAAAAAAAAACAAAAAAAAA
AATTATAAAAACTACTAA
Found at i:3943427 original size:13 final size:13
Alignment explanation
Indices: 3943368--3943429 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 13
3943358 AACTTAAATC
*
3943368 AAAACCAAAC-AA
1 AAAAACAAACAAA
3943380 AAAAACAAA-AAA
1 AAAAACAAACAAA
3943392 AAAAA-AATAC-AA
1 AAAAACAA-ACAAA
**
3943404 AAAAAGTAACAAA
1 AAAAACAAACAAA
3943417 AAAAACAAACAAA
1 AAAAACAAACAAA
3943430 CTTTACATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
11 2 0.05
12 25 0.61
13 14 0.34
ACGTcount: A:0.82, C:0.13, G:0.02, T:0.03
Consensus pattern (13 bp):
AAAAACAAACAAA
Found at i:3943505 original size:21 final size:21
Alignment explanation
Indices: 3943481--3943641 Score: 68
Period size: 19 Copynumber: 7.5 Consensus size: 21
3943471 TTCCAACCAC
3943481 AACAAAAAAAACTAAACTAAAA
1 AACAAAAAAAACTAAACT-AAA
3943503 ACACAAAAAAAAC-AACAC-AAA
1 A-ACAAAAAAAACTAA-ACTAAA
*
3943524 ACACAAAAGAAAA-AAAACTAAA
1 A-ACAAAA-AAAACTAAACTAAA
** * * *
3943546 CTCATACTAAATACAAAAACATAAA
1 AACA-A-AAAAAAC-TAAAC-TAAA
* *
3943571 AAAAAAAAACAACATAAACTAAT
1 AACAAAAAA-AAC-TAAACTAAA
*
3943594 AA-AAAAAAAA--AGACTAAA
1 AACAAAAAAAACTAAACTAAA
*
3943612 AAAAAAAAAAACT-AA-TAAA
1 AACAAAAAAAACTAAACTAAA
*
3943631 AATAAAAAAAA
1 AACAAAAAAAA
3943642 ACAACCAAAA
Statistics
Matches: 110, Mismatches: 15, Indels: 31
0.71 0.10 0.20
Matches are distributed among these distances:
18 8 0.07
19 22 0.20
20 1 0.01
21 17 0.15
22 22 0.20
23 22 0.20
24 13 0.12
25 5 0.05
ACGTcount: A:0.76, C:0.13, G:0.01, T:0.09
Consensus pattern (21 bp):
AACAAAAAAAACTAAACTAAA
Found at i:3943512 original size:23 final size:22
Alignment explanation
Indices: 3943482--3943545 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
3943472 TCCAACCACA
3943482 ACAAAAAAAACTAAACTAAAAAC
1 ACAAAAAAAAC-AAACTAAAAAC
3943505 ACAAAAAAAAC-AAC-ACAAAAC
1 ACAAAAAAAACAAACTA-AAAAC
*
3943526 ACAAAAGAAAAAAAACTAAA
1 ACAAAA-AAAACAAACTAAA
3943546 CTCATACTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 1 0.03
21 14 0.39
22 4 0.11
23 16 0.44
24 1 0.03
ACGTcount: A:0.77, C:0.17, G:0.02, T:0.05
Consensus pattern (22 bp):
ACAAAAAAAACAAACTAAAAAC
Found at i:3943577 original size:40 final size:38
Alignment explanation
Indices: 3943528--3943664 Score: 130
Period size: 41 Copynumber: 3.4 Consensus size: 38
3943518 CACAAAACAC
* * *
3943528 AAAAGAAAAAAAACTAAACTCATACTAAATACAAAAACATA
1 AAAAAAAAAAAAACTAAACT-A-A-TAAAAAAAAAAACATA
*
3943569 AAAAAAAAAAACAACATAAACTAATAAAAAAAAAAAGACTA
1 AAAAAAAAAAA-AAC-TAAACTAATAAAAAAAAAAACA-TA
** *
3943610 AAAAAAAAAAAAACTAATAAAAATAAAAAAAAACAACCAAA
1 AAAAAAAAAAAAACTAA-ACTAATAAAAAAAAA-AA-CATA
3943651 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
3943665 ACATAAATAT
Statistics
Matches: 82, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
39 3 0.04
40 27 0.33
41 41 0.50
42 5 0.06
43 6 0.07
ACGTcount: A:0.78, C:0.11, G:0.01, T:0.09
Consensus pattern (38 bp):
AAAAAAAAAAAAACTAAACTAATAAAAAAAAAAACATA
Found at i:3943586 original size:18 final size:18
Alignment explanation
Indices: 3943563--3943722 Score: 70
Period size: 19 Copynumber: 7.9 Consensus size: 18
3943553 TAAATACAAA
3943563 AACATAAAAAAAAAAAAC
1 AACATAAAAAAAAAAAAC
*
3943581 AACATAAACTAATAAAAAAAAA
1 AACAT-AA--AA-AAAAAAAAC
*
3943603 AAGACTAAAAAAAAAAAA-
1 AACA-TAAAAAAAAAAAAC
3943621 AACTAATAAAAATAAAAAAAAAC
1 AAC--AT--AAA-AAAAAAAAAC
* *
3943644 AACCAAAAAAAAAAAAAAA
1 AA-CATAAAAAAAAAAAAC
* *
3943663 ACACATAAATATAAGAAAAC
1 A-ACATAAA-AAAAAAAAAC
* *
3943683 TACAAAAACTAAAAACTAAAAC
1 AACATAAA--AAAAA--AAAAC
*
3943705 AACTTAAAAACAAAAAAA
1 AACATAAAAA-AAAAAAA
3943723 AAAACACGCA
Statistics
Matches: 108, Mismatches: 16, Indels: 35
0.68 0.10 0.22
Matches are distributed among these distances:
18 7 0.06
19 36 0.33
20 20 0.19
21 8 0.07
22 33 0.31
23 3 0.03
24 1 0.01
ACGTcount: A:0.78, C:0.11, G:0.01, T:0.10
Consensus pattern (18 bp):
AACATAAAAAAAAAAAAC
Found at i:3943598 original size:1 final size:1
Alignment explanation
Indices: 3943594--3943663 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
3943584 ATAAACTAAT
* ** ** * * * **
3943594 AAAAAAAAAAAGACTAAAAAAAAAAAAAACTAATAAAAATAAAAAAAAACAACCAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3943659 AAAAA
1 AAAAA
3943664 CACATAAATA
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.07, G:0.01, T:0.06
Consensus pattern (1 bp):
A
Found at i:3943601 original size:23 final size:21
Alignment explanation
Indices: 3943569--3943770 Score: 116
Period size: 23 Copynumber: 9.5 Consensus size: 21
3943559 CAAAAACATA
3943569 AAAAAAAAAAACAACATAAAC
1 AAAAAAAAAAACAACATAAAC
*
3943590 TAATAAAAAAAAA-AAGACTAAA-
1 -AA-AAAAAAAAACAACA-TAAAC
*
3943612 AAAAAAAAAAACTA-ATAAA-
1 AAAAAAAAAAACAACATAAAC
*
3943631 AATAAAAAAAAACAACCA-AAAA
1 AA-AAAAAAAAACAA-CATAAAC
3943653 AAAAAAAAAAAC-ACAT-AA-
1 AAAAAAAAAAACAACATAAAC
* * * * *
3943671 ATATAAGAAAACTACAAAAAC
1 AAAAAAAAAAACAACATAAAC
** *
3943692 TAAAAACTAAAACAACTTAAAAAC
1 -AAAAAAAAAAACAAC--ATAAAC
* *
3943716 AAAAAAAAAAACACGCAAAAAC
1 AAAAAAAAAAACA-ACATAAAC
3943738 AAAAAAAAAAAACAACA-ACAAC
1 -AAAAAAAAAAACAACATA-AAC
*
3943760 AAACAAAAAAA
1 AAAAAAAAAAA
3943771 TGTAAAAAAA
Statistics
Matches: 146, Mismatches: 17, Indels: 35
0.74 0.09 0.18
Matches are distributed among these distances:
18 9 0.06
19 13 0.09
20 24 0.16
21 27 0.18
22 29 0.20
23 37 0.25
24 7 0.05
ACGTcount: A:0.78, C:0.13, G:0.01, T:0.07
Consensus pattern (21 bp):
AAAAAAAAAAACAACATAAAC
Found at i:3943615 original size:16 final size:16
Alignment explanation
Indices: 3943572--3943812 Score: 104
Period size: 16 Copynumber: 14.4 Consensus size: 16
3943562 AAACATAAAA
3943572 AAAAAAAACAACATAAACT
1 AAAAAAAA-AA-A-AAACT
3943591 AATAAAAAAAAAAAGACT
1 AA-AAAAAAAAAAA-ACT
3943609 AAAAAAAAAAAAAACT
1 AAAAAAAAAAAAAACT
3943625 AATAAAAATAAAAAAA--
1 AA-AAAAA-AAAAAAACT
3943641 AACAACCAAAAAAAAAA--
1 AA-AA--AAAAAAAAAACT
* *
3943658 AAAAAACACATAAATA-T
1 AAAAAA-A-AAAAAAACT
* *
3943675 AAGAAAACTACAAAAACT
1 AA-AAAA-AAAAAAAACT
** *
3943693 AAAAACTAAAACAACT
1 AAAAAAAAAAAAAACT
* *
3943709 TAAAAACAAAAAAA--
1 AAAAAAAAAAAAAACT
* ***
3943723 AAAACACGCAAAAAC-
1 AAAAAAAAAAAAAACT
3943738 AAAAAAAAAAAACAAC-
1 AAAAAAAAAAAA-AACT
*
3943754 AACAACAAACAAAAAAATGT
1 AA-AA-AAA-AAAAAAA-CT
3943774 AAAAAAAAAAAAAACT
1 AAAAAAAAAAAAAACT
* *
3943790 AACAAAAAAACAAACT
1 AAAAAAAAAAAAAACT
3943806 AAAAAAA
1 AAAAAAA
3943813 CTATCTTTAG
Statistics
Matches: 178, Mismatches: 26, Indels: 39
0.73 0.11 0.16
Matches are distributed among these distances:
14 12 0.07
15 9 0.05
16 60 0.34
17 46 0.26
18 32 0.18
19 11 0.06
20 8 0.04
ACGTcount: A:0.78, C:0.12, G:0.02, T:0.08
Consensus pattern (16 bp):
AAAAAAAAAAAAAACT
Found at i:3943616 original size:19 final size:18
Alignment explanation
Indices: 3943570--3943812 Score: 102
Period size: 18 Copynumber: 12.4 Consensus size: 18
3943560 AAAAACATAA
3943570 AAAAAAAAAACAACATAAACT
1 AAAAAAAAAA-AA-A-AAACT
* *
3943591 AATAAAAAAAAAAAGACT
1 AAAAAAAAAAAAAAAACT
3943609 AAAAAAAAAAAAAACTAA-T
1 AAAAAAAAAAAAAA--AACT
*
3943628 AAAAATAAAAAAAAACAACC
1 AAAAA-AAAAAAAAA-AACT
3943648 AAAAAAAAAAAAAAAAC-
1 AAAAAAAAAAAAAAAACT
* * * *
3943665 ACATAAATATAAGAAAACT
1 A-AAAAAAAAAAAAAAACT
3943684 ACAAAAACTAAAAACTAAAACAACTT
1 --AAAAA--AAAAA--AAAA-AAC-T
*
3943710 AAAAACAAAAAAAAAAACACGCA
1 -AAAA-AAAAAAAAAAA-A--CT
3943733 AAAACAAAAAAAAAAAAC-
1 AAAA-AAAAAAAAAAAACT
3943751 AACAACAACAAACAAAAAAA-T
1 AA-AA-AA-AAA-AAAAAAACT
**
3943772 GTAAAAAAAAAAAAAACT
1 AAAAAAAAAAAAAAAACT
* *
3943790 --AACAAAAAAACAAACT
1 AAAAAAAAAAAAAAAACT
3943806 AAAAAAA
1 AAAAAAA
3943813 CTATCTTTAG
Statistics
Matches: 176, Mismatches: 21, Indels: 53
0.70 0.08 0.21
Matches are distributed among these distances:
16 14 0.08
17 8 0.05
18 42 0.24
19 26 0.15
20 25 0.14
21 19 0.11
22 24 0.14
24 9 0.05
25 7 0.04
26 2 0.01
ACGTcount: A:0.78, C:0.12, G:0.02, T:0.08
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAACT
Found at i:3943656 original size:84 final size:82
Alignment explanation
Indices: 3943568--3943799 Score: 232
Period size: 84 Copynumber: 2.8 Consensus size: 82
3943558 ACAAAAACAT
3943568 AAAAAAAAAAAACAACATAAACTAATAAAAAAAAAAAGACTAAAAAAAAAAAAAACTAATAAAAA
1 AAAAAAAAAAAACAACATAAACTAATAAAAAAAAAAAGACTAAAAAAAAAAAAAACTAA-AAAAA
3943633 TAAAAAAAAACAAC-CAAAA
65 -AAAAAAAAAC-ACGCAAAA
** *
3943652 AAAAAAAAAAAAC-ACATAAA-T-ATAAGAAAACTACAAAA-ACTAAAAACTAAAACAACTTAAA
1 AAAAAAAAAAAACAACATAAACTAATAA-AAAA--A-AAAAGACTAAAAAAAAAAAAAAC-TAAA
3943713 AACAAAAAAAAAAACACGCAAAA
61 AA-AAAAAAAAAAACACGCAAAA
* * * *
3943736 ACAAAAAAAAAA-AACA-ACAAC-AACAAACAAAAAAATG--TAAAAAAAAAAAAAACTAACAAA
1 AAAAAAAAAAAACAACATA-AACTAATAAA-AAAAAAAAGACTAAAAAAAAAAAAAACTAAAAAA
3943796 AAAA
64 AAAA
3943800 CAAACTAAAA
Statistics
Matches: 125, Mismatches: 10, Indels: 31
0.75 0.06 0.19
Matches are distributed among these distances:
79 5 0.04
80 5 0.04
81 17 0.14
82 8 0.06
83 11 0.09
84 64 0.51
85 15 0.12
ACGTcount: A:0.78, C:0.12, G:0.02, T:0.08
Consensus pattern (82 bp):
AAAAAAAAAAAACAACATAAACTAATAAAAAAAAAAAGACTAAAAAAAAAAAAAACTAAAAAAAA
AAAAAAAACACGCAAAA
Found at i:3943673 original size:39 final size:39
Alignment explanation
Indices: 3943568--3943751 Score: 122
Period size: 43 Copynumber: 4.4 Consensus size: 39
3943558 ACAAAAACAT
*
3943568 AAAAAAAAAAAACAACATAAACTAATAAAAAAA-AAAAGACTAA
1 AAAAAAAAAAAACAACATAAA-TAA-AAAAAAACAACA-A--AA
* *
3943611 AAAAAAAAAAAACTAATAAAAATAAAAAAAAACAACCAAAA
1 AAAAAAAAAAAAC-AACATAAATAAAAAAAAACAA-CAAAA
* * *
3943652 AAAAAAAAAAAAC-ACATAAATATAAGAAAACTACAAAA
1 AAAAAAAAAAAACAACATAAATAAAAAAAAACAACAAAA
** * * *
3943690 ACTAAAAACTAAAACAACTTAAAAACAAAAAAAAAAACACGCAAA
1 A--AAAAAAAAAAACAACATAAATA-AAAAAAAACAACA---AAA
3943735 AACAAAAAAAAAA-AACA
1 AA-AAAAAAAAAACAACA
3943752 ACAACAACAA
Statistics
Matches: 111, Mismatches: 19, Indels: 22
0.73 0.12 0.14
Matches are distributed among these distances:
38 6 0.05
39 15 0.14
40 10 0.09
41 22 0.20
42 16 0.14
43 23 0.21
44 15 0.14
45 4 0.04
ACGTcount: A:0.78, C:0.12, G:0.02, T:0.08
Consensus pattern (39 bp):
AAAAAAAAAAAACAACATAAATAAAAAAAAACAACAAAA
Found at i:3943687 original size:126 final size:129
Alignment explanation
Indices: 3943484--3943746 Score: 296
Period size: 124 Copynumber: 2.1 Consensus size: 129
3943474 CAACCACAAC
3943484 AAAAAAAACTAAACTAAAAACACAAAAAAAACAACACAAAACACAAAAGAAAAAAAACTAAACTC
1 AAAAAAAACTAAACTAAAAACACAAAAAAAACAACACAAAACACAAAAGAAAAAAAACTAAACTC
* * * *
3943549 ATACTAAATACAAAAACATAAAAAAAAAAAACAACATAAACTAATAAAAAAAAAAAGAC-TAAAA
66 ATACAAAATACAAAAAC-T-AAAAAAAAAAACAACATAAA--AACAAAAAAAAAAACACGCAAAA
3943613 A-A
127 ACA
*
3943615 AAAAAAAACT-AA-TAAAAATA-AAAAAAAACAAC-CAAAA-A-AAAA-AAAAAAACACATAAA-
1 AAAAAAAACTAAACTAAAAACACAAAAAAAACAACACAAAACACAAAAGAAAAAAA-AC-TAAAC
* ** *
3943672 T-ATAAGAAAACTACAAAAACTAAAAACTAAAACAACTTAAAAACAAAAAAAAAAACACGCAAAA
64 TCAT-ACAAAA-TACAAAAACTAAAAAAAAAAACAACATAAAAACAAAAAAAAAAACACGCAAAA
3943736 ACA
127 ACA
3943739 AAAAAAAA
1 AAAAAAAA
3943747 AAACAACAAC
Statistics
Matches: 117, Mismatches: 9, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
122 15 0.13
123 5 0.04
124 35 0.30
125 12 0.10
126 14 0.12
127 5 0.04
128 12 0.10
129 7 0.06
130 2 0.02
131 10 0.09
ACGTcount: A:0.76, C:0.14, G:0.02, T:0.09
Consensus pattern (129 bp):
AAAAAAAACTAAACTAAAAACACAAAAAAAACAACACAAAACACAAAAGAAAAAAAACTAAACTC
ATACAAAATACAAAAACTAAAAAAAAAAACAACATAAAAACAAAAAAAAAAACACGCAAAAACA
Found at i:3943697 original size:40 final size:40
Alignment explanation
Indices: 3943557--3943697 Score: 119
Period size: 41 Copynumber: 3.4 Consensus size: 40
3943547 TCATACTAAA
3943557 TACAAAAACATAAAAAAAAAAAACAACATAAACTAATAAAAAA-
1 TACAAAAAC-TAAAAAAAAAAAAC-ACATAAA-T-ATAAAAAAC
* * *
3943600 -A-AAAAGACTAAAAAAAAAAAAAACTAATAAAAATAAAAAAA
1 TACAAAA-ACTAAAAAAAAAAAACAC--ATAAATATAAAAAAC
* *
3943641 AACAACCAAA-AAAAAAAAAAAAACACATAAATATAAGAAAAC
1 TACAA--AAACTAAAAAAAAAAAACACATAAATATAA-AAAAC
3943683 TACAAAAACTAAAAA
1 TACAAAAACTAAAAA
3943698 CTAAAACAAC
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
40 13 0.16
41 31 0.39
42 17 0.21
43 16 0.20
44 1 0.01
45 2 0.03
ACGTcount: A:0.78, C:0.11, G:0.01, T:0.10
Consensus pattern (40 bp):
TACAAAAACTAAAAAAAAAAAACACATAAATATAAAAAAC
Found at i:3943745 original size:26 final size:26
Alignment explanation
Indices: 3943711--3943799 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
3943701 AAACAACTTA
*
3943711 AAAACAAAAAAAAAAACACGCAA-AAAC
1 AAAA-AAAAAAAAAAACA-ACAACAAAC
*
3943738 AAAAAAAAAAAACAACAACAACAAAC
1 AAAAAAAAAAAAAAACAACAACAAAC
* * *
3943764 AAAAAAATGTAAAAAAAAAAAAAACTAAC
1 AAAAAAA---AAAAAAAACAACAACAAAC
3943793 AAAAAAA
1 AAAAAAA
3943800 CAAACTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
25 3 0.06
26 23 0.44
27 4 0.08
29 22 0.42
ACGTcount: A:0.81, C:0.13, G:0.02, T:0.03
Consensus pattern (26 bp):
AAAAAAAAAAAAAAACAACAACAAAC
Found at i:3943750 original size:46 final size:44
Alignment explanation
Indices: 3943685--3943813 Score: 113
Period size: 46 Copynumber: 2.9 Consensus size: 44
3943675 AAGAAAACTA
* **
3943685 CAAAAACTAAAAACTAAAACAACTTAAAAACAAAAAAAAAAACACG
1 CAAAAACAAAAAAAAAAAACAAC--AAAAACAAAAAAAAAAACACG
* * *
3943731 CAAAAACAAAAAAAAAAAACAACAACAAC-AAACAAAAAA-ATG
1 CAAAAACAAAAAAAAAAAACAACAAAAACAAAAAAAAAAACACG
* * *
3943773 TAAAAA-AAAAAAAAACTAACAA-AAAAACAAACTAAAAAAAC
1 CAAAAACAAAAAAAAA-AAACAACAAAAACAAA-AAAAAAAAC
3943814 TATCTTTAGA
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
41 14 0.21
42 14 0.21
43 15 0.22
44 5 0.07
46 20 0.29
ACGTcount: A:0.77, C:0.16, G:0.02, T:0.06
Consensus pattern (44 bp):
CAAAAACAAAAAAAAAAAACAACAAAAACAAAAAAAAAAACACG
Found at i:3943760 original size:22 final size:22
Alignment explanation
Indices: 3943568--3943770 Score: 92
Period size: 22 Copynumber: 9.5 Consensus size: 22
3943558 ACAAAAACAT
3943568 AAAAAAAAAAAACAACATA-AAC
1 AAAAAAAAAAAACAACA-ACAAC
* *
3943590 TAATAAAAAAAAA-AA-GACTAA-
1 -AAAAAAAAAAAACAACAAC-AAC
*
3943611 AAAAAAAAAAAACTAA-TA-AA-
1 AAAAAAAAAAAAC-AACAACAAC
*
3943631 AATAAAAAAAAACAAC--CAA-
1 AAAAAAAAAAAACAACAACAAC
3943650 AAAAAAAAAAAA-AAC-ACATA-
1 AAAAAAAAAAAACAACAACA-AC
* * * * *
3943670 AATATAAGAAAACTACAAAAAC
1 AAAAAAAAAAAACAACAACAAC
* ** *
3943692 TAAAAACTAAAACAACTTAAAAAC
1 AAAAAAAAAAAACAAC--AACAAC
* *
3943716 -AAAAAAAAAAACACGCAAAAAC
1 AAAAAAAAAAAACA-ACAACAAC
3943738 AAAAAAAAAAAACAACAACAAC
1 AAAAAAAAAAAACAACAACAAC
*
3943760 AAACAAAAAAA
1 AAAAAAAAAAA
3943771 TGTAAAAAAA
Statistics
Matches: 142, Mismatches: 23, Indels: 31
0.72 0.12 0.16
Matches are distributed among these distances:
18 3 0.02
19 17 0.12
20 36 0.25
21 3 0.02
22 41 0.29
23 35 0.25
24 7 0.05
ACGTcount: A:0.78, C:0.13, G:0.01, T:0.07
Consensus pattern (22 bp):
AAAAAAAAAAAACAACAACAAC
Found at i:3943813 original size:13 final size:12
Alignment explanation
Indices: 3943710--3943813 Score: 65
Period size: 12 Copynumber: 8.5 Consensus size: 12
3943700 AAAACAACTT
*
3943710 AAAAACAAAAAA
1 AAAAACAAACAA
**
3943722 AAAAACACGCAA
1 AAAAACAAACAA
3943734 AAACAA-AAA-AA
1 AAA-AACAAACAA
3943745 AAAAAC-AACAA
1 AAAAACAAACAA
3943756 CAACAAACAAA-AA
1 -AA-AAACAAACAA
*
3943769 AATGTAAA-AAAAAA
1 AA---AAACAAACAA
*
3943783 AAAAACTAACAA
1 AAAAACAAACAA
3943795 AAAAACAAACTAA
1 AAAAACAAAC-AA
3943808 AAAAAC
1 AAAAAC
3943814 TATCTTTAGA
Statistics
Matches: 72, Mismatches: 9, Indels: 21
0.71 0.09 0.21
Matches are distributed among these distances:
10 4 0.06
11 10 0.14
12 30 0.42
13 19 0.26
14 9 0.12
ACGTcount: A:0.80, C:0.14, G:0.02, T:0.04
Consensus pattern (12 bp):
AAAAACAAACAA
Found at i:3943856 original size:22 final size:22
Alignment explanation
Indices: 3943823--3943873 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
3943813 CTATCTTTAG
3943823 AAACAAACAATAATA-ACAAAAA
1 AAACAAACAATAA-ACACAAAAA
3943845 AAACTAAA-AATAAACTACAAAAA
1 AAAC-AAACAATAAAC-ACAAAAA
3943868 AAACAA
1 AAACAA
3943874 TAAAAAAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.04
22 11 0.42
23 14 0.54
ACGTcount: A:0.76, C:0.14, G:0.00, T:0.10
Consensus pattern (22 bp):
AAACAAACAATAAACACAAAAA
Found at i:3944555 original size:203 final size:207
Alignment explanation
Indices: 3943878--3944577 Score: 1084
Period size: 203 Copynumber: 3.4 Consensus size: 207
3943868 AAACAATAAA
* *
3943878 AAAGACATAGCTAATTTGGCTTTCACGTG-TTACGTTAAAGCAAGTCTAAGATGATTTGGCATCT
1 AAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCT
*
3943942 C-GTATTGTCAGAGAACAAATCGAAGTTTGGAGTCTCCATATTCGACGGAGGGCAGACACATAGC
66 CTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
3944006 AGATCTGGCCTTCAGATGTTTATG-CTGAAGCAAGATCCAAGAT-G-TTGGCATCCTTGTGCTTA
131 AGATCTGGCCTTCAGATGTTTA-GACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTA
3944068 CAAGGAACAAATC
195 CAAGGAACAAATC
* * *
3944081 GAAGACATA-ATGATTT--C-TTCACGTGTTTATGTTGAAGCAAGTCTAAGATGATTTGGCATCT
1 AAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCT
* *
3944142 CTGTATTGTCAGAAAACAAATCGAAGTTTGGCGTTTCCATATTCGACGGAGGGCAGACACATAGC
66 CTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
* *
3944207 AGATCTGGCCTCCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
131 AGATCTGGCCTTCAGATGTTTAGACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
3944272 AAGGAACAAATC
196 AAGGAACAAATC
*
3944284 GAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCT
1 AAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCT
* *
3944349 CTGTATTGTCA-AGAACAAATCGAAGTTTGGCGTCTCCATATT-GACGGAGGACAGACATATAGC
66 CTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
** * * *
3944412 AGATCTAACCTTCAGATGATTAGACTGAAGC-AGATCCAATATGGTTTGGTATCCTTGTGCTTAC
131 AGATCTGGCCTTCAGATGTTTAGACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
*
3944476 AAGGAGCAAATC
196 AAGGAACAAATC
* * *
3944488 AAAGACATAGCTGA-TTGGCTTTCGCGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCT
1 AAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCT
* *
3944552 CTGTATTGTCAGGGAACAAATTGAAG
66 CTGTATTGTCAGAGAACAAATCGAAG
3944578 AAGCAGATTT
Statistics
Matches: 457, Mismatches: 30, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
199 8 0.02
200 35 0.08
201 100 0.22
202 6 0.01
203 106 0.23
204 73 0.16
205 45 0.10
206 30 0.07
207 54 0.12
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (207 bp):
AAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCT
CTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
AGATCTGGCCTTCAGATGTTTAGACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
AAGGAACAAATC
Found at i:3944988 original size:19 final size:19
Alignment explanation
Indices: 3944963--3945053 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
3944953 TATATCTTCA
3944963 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
3944982 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
3945001 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
3945018 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
3945036 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
3945054 AGATATGATT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 34 0.52
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:3945003 original size:14 final size:15
Alignment explanation
Indices: 3944984--3945039 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
3944974 TCTTAGATGT
3944984 GATATG-CAATCTTA
1 GATATGACAATCTTA
3944998 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
3945015 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
3945033 GATATGA
1 GATATGA
3945040 TATACAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:3945033 original size:35 final size:37
Alignment explanation
Indices: 3944971--3945060 Score: 134
Period size: 35 Copynumber: 2.5 Consensus size: 37
3944961 CAATGATATG
*
3944971 CAATCTTAGATGTGATATGCAATCTTAGATATG-ATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGAATA
3945007 CAATCTTAGATATGAT-TGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGA-ATA
3945044 CAATCTTAGA-A-GATATG
1 CAATCTTAGATATGATATG
3945061 ATTTTGTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
35 19 0.38
36 18 0.36
37 13 0.26
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (37 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGAATA
Done.