Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 13 of 132
Found at i:3699073 original size:30 final size:30
Alignment explanation
Indices: 3699039--3699359 Score: 470
Period size: 30 Copynumber: 10.7 Consensus size: 30
3699029 AACAATTCGG
* * **
3699039 AAATTGCATTTTAACCCTGAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
3699069 AAATTATATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
3699099 AAATTACATTTCGACCTCAAAAC-TTTCCAA
1 AAATTACATTTTGACCCCAAAACTTTTCC-A
*
3699129 AAATTACATTTTGA-CCCAAAAATTCTTCCA
1 AAATTACATTTTGACCCCAAAACTT-TTCCA
*
3699159 AAATTACATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
3699189 AAATTACATTTTGACCCCAAAGCTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
3699219 AAATTACATTTTGACCTCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
3699249 AAATTATATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
3699279 AAATTACATTTTGACCCCAAAAC-TTTCCAA
1 AAATTACATTTTGACCCCAAAACTTTTCC-A
3699309 AAATTACATTTTGACCCCAAAAC-TTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
3699338 AAATTACATTTTGACCCCAAAA
1 AAATTACATTTTGACCCCAAAA
3699360 ATTTCCTAAA
Statistics
Matches: 266, Mismatches: 20, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
29 39 0.15
30 214 0.80
31 13 0.05
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.33
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTCCA
Found at i:3699407 original size:59 final size:57
Alignment explanation
Indices: 3699096--3699585 Score: 261
Period size: 60 Copynumber: 8.3 Consensus size: 57
3699086 CAAAACTTTT
* * * * ** * *
3699096 CCAAAATTA-CATTTCGACCTCAAAACTTTCCAAAAATTACATTTTGACCCAAAAATTCTT
1 CCAAAATTACCATTTTGACCCCAAAACTTT-C-AAAATTCCATTTTAACCC-CGATTTC-A
* * * * *
3699156 CCAAAATTA-CATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAGCTTT-T
1 CCAAAATTACCATTTTGACCCCAAAAC-TTT-CAAAATTCCATTTTAACCCC---GATTTCA
* ** * * *
3699216 CCAAAATTA-CATTTTGACCTCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTT-T
1 CCAAAATTACCATTTTGACCCCAAAAC-TTT-CAAAATTCCATTTTAACCCC--GA-TTTCA
* * *
3699276 CCAAAATTA-CATTTTGACCCCAAAACTTTCCAAAAATTACATTTTGACCCCAAAACTTT--
1 CCAAAATTACCATTTTGACCCCAAAACTTT-C-AAAATTCCATTTTAACCCC--GA-TTTCA
* * *
3699335 CCAAAATTA-CATTTTGACCCCAAAAATTTCCTAAATCCCATTTTAACCCCGATTTCA
1 CCAAAATTACCATTTTGACCCCAAAACTTT-CAAAATTCCATTTTAACCCCGATTTCA
* * * **
3699392 CCAAAATTTACCATTTT-ACCCCCGAAGC-TTCTGAAATTCTGTTTTAACCCCGATTTCA
1 CCAAAA-TTACCATTTTGA-CCCCAAAACTTTC-AAAATTCCATTTTAACCCCGATTTCA
* * * *
3699450 CTAAAAATTACCATTTT-ACCCCCGAAACCTTT-AAAATTCTAATTTTAACCCCAATTTCA
1 C-CAAAATTACCATTTTGA-CCCC-AAAACTTTCAAAATTC-CATTTTAACCCCGATTTCA
* ** *
3699509 CCAAAATTTACCATTTTTACCCCCGAAGCCTTT-AAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAA-TTACCATTTTGA-CCCC-AAAACTTTCAAAATTCCA-TTTTAACCCCGATTTCA
3699569 CCAAAATTACCATTTTG
1 CCAAAATTACCATTTTG
3699586 CCCTCGGATA
Statistics
Matches: 372, Mismatches: 39, Indels: 39
0.83 0.09 0.09
Matches are distributed among these distances:
55 3 0.01
56 1 0.00
57 7 0.02
58 70 0.19
59 94 0.25
60 190 0.51
61 5 0.01
62 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (57 bp):
CCAAAATTACCATTTTGACCCCAAAACTTTCAAAATTCCATTTTAACCCCGATTTCA
Found at i:3699470 original size:29 final size:30
Alignment explanation
Indices: 3699372--3699584 Score: 97
Period size: 29 Copynumber: 7.2 Consensus size: 30
3699362 TTCCTAAATC
* *
3699372 CCATTTTAACCCCGATTTCACCAAAATTTA
1 CCATTTTAACCCCGATTTCACTAAAAATTA
* * *
3699402 CCATTTTACCCCCGAAGCTT--CT-GAAATT-
1 CCATTTTAACCCCG-A-TTTCACTAAAAATTA
**
3699430 CTGTTTTAACCCCGATTTCACTAAAAATTA
1 CCATTTTAACCCCGATTTCACTAAAAATTA
* ** *
3699460 CCATTTTACCCCCGA-AAC-CTTTAAAATT-
1 CCATTTTAACCCCGATTTCAC-TAAAAATTA
* * * *
3699488 CTAATTTTAACCCCAATTTCACCAAAATTTA
1 C-CATTTTAACCCCGATTTCACTAAAAATTA
* ** *
3699519 CCATTTTTACCCCCGA-AGC-CTTTAAAATT-
1 CCA-TTTTAACCCCGATTTCAC-TAAAAATTA
* *
3699548 CTATTTTTAACCCCGATTTCAC-CAAAATTA
1 CCA-TTTTAACCCCGATTTCACTAAAAATTA
3699578 CCATTTT
1 CCATTTT
3699585 GCCCTCGGAT
Statistics
Matches: 129, Mismatches: 38, Indels: 33
0.64 0.19 0.17
Matches are distributed among these distances:
26 2 0.02
27 1 0.01
28 15 0.12
29 53 0.41
30 42 0.33
31 14 0.11
32 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (30 bp):
CCATTTTAACCCCGATTTCACTAAAAATTA
Found at i:3699550 original size:60 final size:59
Alignment explanation
Indices: 3699374--3699584 Score: 320
Period size: 58 Copynumber: 3.6 Consensus size: 59
3699364 CCTAAATCCC
*
3699374 ATTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGAAG-CTTCTGAAATTCT-
1 ATTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGAAGCCTT-TAAAATTCTA
* * * *
3699432 GTTTTAACCCCGATTTCACTAAAAATTACCATTTTACCCCCGAAACCTTTAAAATTCTA
1 ATTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGAAGCCTTTAAAATTCTA
*
3699491 ATTTTAACCCCAATTTCACCAAAATTTACCATTTTTACCCCCGAAGCCTTTAAAATTCTA
1 ATTTTAACCCCGATTTCACCAAAATTTACCA-TTTTACCCCCGAAGCCTTTAAAATTCTA
*
3699551 TTTTTAACCCCGATTTCACCAAAA-TTACCATTTT
1 ATTTTAACCCCGATTTCACCAAAATTTACCATTTT
3699585 GCCCTCGGAT
Statistics
Matches: 138, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
58 53 0.38
59 36 0.26
60 49 0.36
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.36
Consensus pattern (59 bp):
ATTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGAAGCCTTTAAAATTCTA
Found at i:3711549 original size:69 final size:69
Alignment explanation
Indices: 3711438--3712058 Score: 919
Period size: 69 Copynumber: 9.0 Consensus size: 69
3711428 CTGCAGGTCT
*
3711438 CAACGCCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
3711503 AGAG
66 AGAG
* *
3711507 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGAA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
3711572 AGAG
66 AGAG
* * * * * *
3711576 CAACGTCATCCCCTCGAAATTGAAATAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
3711640 AGAG
66 AGAG
3711644 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
3711709 AGAG
66 AGAG
*
3711713 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
3711778 AGAG
66 AGAG
* * * * * * *
3711782 CAACGTCATCCCCTCGGAATTGAAATAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
3711846 AGAG
66 AGAG
*
3711850 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
3711915 AGAG
66 AGAG
* * * * * * * **
3711919 CAATGTCATCCCCTTAAAATTTAAGTAGAG-TGGATAACACGCCTACATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
*
3711983 AGAA
66 AGAG
* *
3711987 CAGCGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAAT-ACA-CCTTTATCTCTGAAATTGAAG
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCA-AGTCTTTATCTCTGAAATTGAAG
3712050 TAAGAG
64 TAAGAG
3712056 CAA
1 CAA
3712059 GATCATTTCC
Statistics
Matches: 491, Mismatches: 56, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
68 178 0.36
69 312 0.64
70 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (69 bp):
CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
AGAG
Found at i:3711685 original size:137 final size:137
Alignment explanation
Indices: 3711438--3712058 Score: 915
Period size: 137 Copynumber: 4.5 Consensus size: 137
3711428 CTGCAGGTCT
*
3711438 CAACGCCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
* * * *
3711503 AGAGCAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
66 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTCATCTCTGAAATTGA
*
3711568 AGAAAGAG
130 AGTAAGAG
* * * * * *
3711576 CAACGTCATCCCCTCGAAATTGAAATAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
* * *
3711640 AGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
66 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTCATCTCTGAAATTGA
3711705 AGTAAGAG
130 AGTAAGAG
*
3711713 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
* * * *
3711778 AGAGCAACGTCATCCCCTCGGAATTGAAATAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
66 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAA
3711843 GTAAGAG
131 GTAAGAG
*
3711850 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
* * * * * *
3711915 AGAGCAATGTCATCCCCTTAAAATTTAAGTAGAGTGGATAACACGCCTACATCTCTGAAATTGAA
66 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAA
*
3711980 GTAAGAA
131 GTAAGAG
* *
3711987 CAGCGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAAT-ACA-CCTTTATCTCTGAAATTGAAG
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCA-AGTCTTTATCTCTGAAATTGAAG
3712050 TAAGAGCAA
64 TAAGAGCAA
3712059 GATCATTTCC
Statistics
Matches: 445, Mismatches: 35, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
137 355 0.80
138 90 0.20
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (137 bp):
CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAA
GTAAGAG
Found at i:3711805 original size:206 final size:206
Alignment explanation
Indices: 3711438--3712058 Score: 1019
Period size: 206 Copynumber: 3.0 Consensus size: 206
3711428 CTGCAGGTCT
*
3711438 CAACGCCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
3711503 AGAGCAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
66 AGAGCAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
*
3711568 AGAAAGAGCAACGTCATCCCCTCGAAATTGAAATAGAGTGGATAACACGTCTTCATCTCTGAAAT
131 AGTAAGAGCAACGTCATCCCCTCGAAATTGAAATAGAGTGGATAACACGTCTTCATCTCTGAAAT
3711633 TGAAGTAAGAG
196 TGAAGTAAGAG
3711644 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
3711709 AGAGCAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
66 AGAGCAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
*
3711774 AGTAAGAGCAACGTCATCCCCTCGGAATTGAAATAGAGTGGATAACACGTCTTCATCTCTGAAAT
131 AGTAAGAGCAACGTCATCCCCTCGAAATTGAAATAGAGTGGATAACACGTCTTCATCTCTGAAAT
3711839 TGAAGTAAGAG
196 TGAAGTAAGAG
*
3711850 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
* * * * * * * * **
3711915 AGAGCAATGTCATCCCCTTAAAATTTAAGTAGAG-TGGATAACACGCCTACATCTCTGAAATTGA
66 AGAGCAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
* * * * * * ** *
3711979 AGTAAGAACAGCGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAATACACCTTTATCTCTGAAA
131 AGTAAGAGCAACGTCATCCCCTCGAAATTGAAATAGAG-TGGATAACACGTCTTCATCTCTGAAA
3712044 TTGAAGTAAGAG
195 TTGAAGTAAGAG
3712056 CAA
1 CAA
3712059 GATCATTTCC
Statistics
Matches: 390, Mismatches: 24, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
205 57 0.15
206 333 0.85
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (206 bp):
CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
AGAGCAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
AGTAAGAGCAACGTCATCCCCTCGAAATTGAAATAGAGTGGATAACACGTCTTCATCTCTGAAAT
TGAAGTAAGAG
Found at i:3712427 original size:11 final size:11
Alignment explanation
Indices: 3712404--3712466 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
3712394 TCAAATTTAT
3712404 TTTAATCTTAAA
1 TTTAAT-TTAAA
*
3712416 TTTATTTTAAA
1 TTTAATTTAAA
*
3712427 TTCAATTTAAA
1 TTTAATTTAAA
*
3712438 TTTAAATTTGAA
1 TTT-AATTTAAA
3712450 TTTAATTTAAA
1 TTTAATTTAAA
3712461 TTTAAT
1 TTTAAT
3712467 GTTATTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 29 0.66
12 15 0.34
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:3712463 original size:17 final size:16
Alignment explanation
Indices: 3712414--3712482 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
3712404 TTTAATCTTA
* *
3712414 AATTTATTTTAAATTC
1 AATTTAATTTAAATTT
3712430 AATTTAAATTTAAATTT
1 AATTT-AATTTAAATTT
3712447 GAATTTAATTTAAATTT
1 -AATTTAATTTAAATTT
3712464 AATGTT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
3712481 AA
1 AA
3712483 AAAGAAAGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 11 0.23
17 31 0.66
18 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:3712483 original size:6 final size:6
Alignment explanation
Indices: 3712411--3712465 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
3712401 TATTTTAATC
* * *
3712411 TTAAAT TT-ATT TTAAA- TTCAAT TTAAAT TTAAAT TTGAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
3712456 TTAAAT TTAA
1 TTAAAT TTAA
3712466 TGTTATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
5 13 0.32
6 28 0.68
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:3712690 original size:20 final size:20
Alignment explanation
Indices: 3712661--3712719 Score: 100
Period size: 20 Copynumber: 2.9 Consensus size: 20
3712651 TGCCTACTGT
*
3712661 TGCTGGCCACCAGCTCCATC
1 TGCTGACCACCAGCTCCATC
3712681 TGCTGACCACCAGCTCCATC
1 TGCTGACCACCAGCTCCATC
3712701 TGCTGACCACCAAGCTCCA
1 TGCTGACCACC-AGCTCCA
3712720 CCATGCCCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 30 0.81
21 7 0.19
ACGTcount: A:0.20, C:0.44, G:0.17, T:0.19
Consensus pattern (20 bp):
TGCTGACCACCAGCTCCATC
Found at i:3713267 original size:16 final size:16
Alignment explanation
Indices: 3713229--3713270 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3713219 TAGTAGCTAA
* * *
3713229 AATATTAATAACTATT
1 AATAATAATAAATATC
3713245 AAT-ATAATAAATATC
1 AATAATAATAAATATC
3713260 AATAATAATAA
1 AATAATAATAA
3713271 CAATAATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAATAATAAATATC
Found at i:3714474 original size:30 final size:30
Alignment explanation
Indices: 3714440--3714700 Score: 393
Period size: 30 Copynumber: 8.7 Consensus size: 30
3714430 AACAATTCGG
* * *
3714440 AAATTGCATTTTAACCCCGAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
3714470 AAATTATATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
3714500 AAATTACATTTCGACCCCAAAAC-TTTCCAA
1 AAATTACATTTTGACCCCAAAACTTTTCC-A
* *
3714530 AAATTACATTTTGACCCAAAAACTCTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
3714560 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
3714590 AAATTACATTTTGACCCCAAAGCTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
3714620 AAATTACATTTTGACCCCAAAAC-TTTCCAA
1 AAATTACATTTTGACCCCAAAACTTTTCC-A
* *
3714650 AAATTACATTTTGACCCTAAAAC-TTTCAA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
3714679 AAATTACATTTTGACCCCAAAA
1 AAATTACATTTTGACCCCAAAA
3714701 ATTTCCTAAA
Statistics
Matches: 212, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
29 32 0.15
30 176 0.83
31 4 0.02
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTCCA
Found at i:3714581 original size:19 final size:19
Alignment explanation
Indices: 3714557--3714610 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 19
3714547 AAAAACTCTT
3714557 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
3714576 CC-AAA--AC-TTTT----
1 CCAAAATTACATTTTGACC
3714587 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
3714606 CCAAA
1 CCAAA
3714611 GCTTTTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 16
0.63 0.00 0.37
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
14 2 0.07
15 8 0.30
16 2 0.07
18 3 0.11
19 7 0.26
ACGTcount: A:0.39, C:0.28, G:0.04, T:0.30
Consensus pattern (19 bp):
CCAAAATTACATTTTGACC
Found at i:3714748 original size:59 final size:57
Alignment explanation
Indices: 3714678--3714906 Score: 214
Period size: 59 Copynumber: 3.9 Consensus size: 57
3714668 AAAACTTTCA
*
3714678 AAAATTA-CATTTTGACCCCAAAAATTTCCTAAATCCCA-TTTTAACCCCGATTTCACC
1 AAAATTACCATTTT-ACCCCAAAAATTT-CTAAATTCCATTTTTAACCCCGATTTCACC
* ** *
3714735 AAAATTTACCATTTTACCCCTAAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACTG
1 AAAA-TTACCATTTTACCCCAAAAATTTCT-AAATTCCATTTTTAACCCCGATTTCAC-C
** * *
3714795 AAAATTACCATTTTACCCTCGAAACCTTT-AAAATTCCATTTTTGACCCCGATTTCACC
1 AAAATTACCATTTTACCC-C-AAAAATTTCTAAATTCCATTTTTAACCCCGATTTCACC
* * * * * *
3714853 AAAATTACCATTTTGCCCC-CAAATATCCATAAGTCTCATTTTTCACCCCGATTT
1 AAAATTACCATTTTACCCCAAAAATTTCTA-AATTC-CATTTTTAACCCCGATTT
3714907 TATCATTTAT
Statistics
Matches: 142, Mismatches: 20, Indels: 19
0.78 0.11 0.10
Matches are distributed among these distances:
55 3 0.02
56 1 0.01
57 11 0.08
58 54 0.38
59 64 0.45
60 5 0.04
61 4 0.03
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCAAAAATTTCTAAATTCCATTTTTAACCCCGATTTCACC
Found at i:3714753 original size:29 final size:29
Alignment explanation
Indices: 3714713--3714866 Score: 100
Period size: 29 Copynumber: 5.2 Consensus size: 29
3714703 TTCCTAAATC
3714713 CCATTTTAACCCCGATTTCACCAAAATTTA
1 CCATTTTAACCCCGATTTCACCAAAA-TTA
* *** * *
3714743 CCATTTT-ACCCCTAAAGCTTCTAAAATT-
1 CCATTTTAACCCCGATTTC-ACCAAAATTA
*
3714771 CCATTTTTAACCCCGATTTCACTGAAAATTA
1 CCA-TTTTAACCCCGATTTCAC-CAAAATTA
*** ***
3714802 CCATTTT-ACCCTCGAAACCTTTAAAATT-
1 CCATTTTAACCC-CGATTTCACCAAAATTA
*
3714830 CCATTTTTGACCCCGATTTCACCAAAATTA
1 CCA-TTTTAACCCCGATTTCACCAAAATTA
3714860 CCATTTT
1 CCATTTT
3714867 GCCCCCAAAT
Statistics
Matches: 91, Mismatches: 24, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
28 6 0.07
29 42 0.46
30 40 0.44
31 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.36
Consensus pattern (29 bp):
CCATTTTAACCCCGATTTCACCAAAATTA
Found at i:3718736 original size:21 final size:22
Alignment explanation
Indices: 3718711--3718751 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3718701 CATTTTCAAG
3718711 TTTATAATATGT-TATTTTACT
1 TTTATAATATGTGTATTTTACT
**
3718732 TTTATTTTATGTGTATTTTA
1 TTTATAATATGTGTATTTTA
3718752 TGTACTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (22 bp):
TTTATAATATGTGTATTTTACT
Found at i:3719125 original size:17 final size:16
Alignment explanation
Indices: 3719101--3719134 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3719091 AACAATTTTG
*
3719101 TAAATTTTTTATTTAT
1 TAAATTTTTTATATAT
3719117 TAAATTTTTTTATATAT
1 TAAA-TTTTTTATATAT
3719134 T
1 T
3719135 CATCTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TAAATTTTTTATATAT
Found at i:3726621 original size:21 final size:22
Alignment explanation
Indices: 3726596--3726638 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3726586 CACGTAATCT
3726596 AAAATGAAA-ATT-TTAAGAATA
1 AAAATGAAATATTATTAA-AATA
3726617 AAAATGAAATATTATTAAAATA
1 AAAATGAAATATTATTAAAATA
3726639 GATGCTGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
AAAATGAAATATTATTAAAATA
Found at i:3728615 original size:34 final size:34
Alignment explanation
Indices: 3728572--3728641 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
3728562 TTAAAGGCAA
3728572 ATTGGAGAAAGAACAACAAAAAAAAATGAAAAAG
1 ATTGGAGAAAGAACAACAAAAAAAAATGAAAAAG
3728606 ATTGGAGAAAGAACAACAAAAAAAAATGAAAAAG
1 ATTGGAGAAAGAACAACAAAAAAAAATGAAAAAG
3728640 AT
1 AT
3728642 ATGCCATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.67, C:0.06, G:0.17, T:0.10
Consensus pattern (34 bp):
ATTGGAGAAAGAACAACAAAAAAAAATGAAAAAG
Found at i:3728661 original size:34 final size:33
Alignment explanation
Indices: 3728572--3728666 Score: 104
Period size: 34 Copynumber: 2.8 Consensus size: 33
3728562 TTAAAGGCAA
*
3728572 ATTGGAGAAAGAACAACAAAAAAAAATGAAAAAG
1 ATTGCAGAAAG-ACAACAAAAAAAAATGAAAAAG
*
3728606 ATTGGAGAAAGAACAACAAAAAAAAATGAAAAAG
1 ATTGCAGAAAG-ACAACAAAAAAAAATGAAAAAG
* *
3728640 ATATGCCATAAAG-CTA-AAAAAAAAATG
1 AT-TG-CAGAAAGACAACAAAAAAAAATG
3728667 CAAAGAAGCA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
33 11 0.20
34 38 0.68
35 2 0.04
36 5 0.09
ACGTcount: A:0.65, C:0.07, G:0.16, T:0.12
Consensus pattern (33 bp):
ATTGCAGAAAGACAACAAAAAAAAATGAAAAAG
Found at i:3730141 original size:2 final size:2
Alignment explanation
Indices: 3730136--3730166 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3730126 GTAAAAAAAT
3730136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3730167 GAATATCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3732976 original size:23 final size:23
Alignment explanation
Indices: 3732932--3732981 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
3732922 GTAAAAAATC
3732932 AAATTTATTTTAGATAAATATA-
1 AAATTTATTTTAGATAAATATAT
**
3732954 AAATTTATTTTATTCTAAATATAT
1 AAATTTATTTTA-GATAAATATAT
3732978 AAAT
1 AAAT
3732982 AAATCTACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.50
23 8 0.33
24 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATTTATTTTAGATAAATATAT
Found at i:3740213 original size:13 final size:13
Alignment explanation
Indices: 3740195--3740232 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3740185 TGATTAAGAT
3740195 TATTGAATATGTA
1 TATTGAATATGTA
*
3740208 TATTGAAT-TTTA
1 TATTGAATATGTA
*
3740220 TAGTGAATATGTA
1 TATTGAATATGTA
3740233 ATTAAAGGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (13 bp):
TATTGAATATGTA
Found at i:3740601 original size:12 final size:11
Alignment explanation
Indices: 3740576--3740619 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
3740566 TTTATAATTT
3740576 TAAATTTTTTA
1 TAAATTTTTTA
3740587 TAAATTTTTTAA
1 TAAATTTTTT-A
3740599 TAAATTTTGTT-
1 TAAATTTT-TTA
3740610 TATAATTTTT
1 TA-AATTTTT
3740620 ATGATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 13 0.43
12 15 0.50
13 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TAAATTTTTTA
Found at i:3740643 original size:17 final size:18
Alignment explanation
Indices: 3740566--3740643 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 18
3740556 TTAATAAAAA
*
3740566 TTTATAA-TTTTAAATTT
1 TTTATAATTTTTAAAATT
3740583 TTTATAAATTTTTTAATAAATTTT
1 TTTAT-AA-TTTTT-A-AAA--TT
**
3740607 GTTTATAATTTTTATGATT
1 -TTTATAATTTTTAAAATT
3740626 TTTA-AATTTTTAAAATT
1 TTTATAATTTTTAAAATT
3740643 T
1 T
3740644 AAAAGGGCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
17 17 0.35
18 6 0.12
19 2 0.04
20 4 0.08
21 2 0.04
22 3 0.06
23 5 0.10
24 4 0.08
25 5 0.10
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTATAATTTTTAAAATT
Found at i:3756306 original size:18 final size:18
Alignment explanation
Indices: 3756271--3756306 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3756261 TGTTTTGATT
*
3756271 ACATAATATATAGAAATA
1 ACATAATATAAAGAAATA
*
3756289 ACATAATATAAAGTAATA
1 ACATAATATAAAGAAATA
3756307 TAAACTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (18 bp):
ACATAATATAAAGAAATA
Found at i:3757759 original size:14 final size:14
Alignment explanation
Indices: 3757718--3757759 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3757708 AAAACCATTT
*
3757718 CTTATAATCTATTCG
1 CTTATAATTTATT-G
*
3757733 CTTA-AATTAATTG
1 CTTATAATTTATTG
3757746 CTTATAATTTATTG
1 CTTATAATTTATTG
3757760 TCACTAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 5 0.22
14 14 0.61
15 4 0.17
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (14 bp):
CTTATAATTTATTG
Found at i:3757910 original size:14 final size:15
Alignment explanation
Indices: 3757891--3757919 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3757881 ACTTTATAAA
3757891 AAATATTT-TTGAAT
1 AAATATTTATTGAAT
3757905 AAATATTTATTGAAT
1 AAATATTTATTGAAT
3757920 TTGAGATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AAATATTTATTGAAT
Found at i:3760098 original size:30 final size:30
Alignment explanation
Indices: 3760042--3760103 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
3760032 TGTGTAATGT
* *
3760042 CATACAAATTTTGATTTTATGTAATTTTATA
1 CATACAAATTTTAATTTGATGTAATTTT-TA
3760073 CATA-AAATTTTAATTTGAT-TAAATTTTTA
1 CATACAAATTTTAATTTGATGT-AATTTTTA
3760102 CA
1 CA
3760104 AATCATTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 5 0.18
30 19 0.68
31 4 0.14
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (30 bp):
CATACAAATTTTAATTTGATGTAATTTTTA
Found at i:3768390 original size:72 final size:72
Alignment explanation
Indices: 3768291--3768425 Score: 225
Period size: 72 Copynumber: 1.9 Consensus size: 72
3768281 GTGTTGAATC
* * *
3768291 TCTCCCATAACAAGCTCTTTGGTGAACTGTCTCCAGAATTAACAAAACTTACAGCTCTGGAAGCC
1 TCTCCCATAACAAGCTCTTTGGCGAACTATCTCCAGAATTAACAAAACTTACAACTCTGGAAGCC
3768356 TTGGATG
66 TTGGATG
* *
3768363 TCTCCCATAACAAGCTCTTTGGCGAACTATGTCCAGAATTAACAAAACTTACAATTCTGGAAG
1 TCTCCCATAACAAGCTCTTTGGCGAACTATCTCCAGAATTAACAAAACTTACAACTCTGGAAG
3768426 TATTCGACGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (72 bp):
TCTCCCATAACAAGCTCTTTGGCGAACTATCTCCAGAATTAACAAAACTTACAACTCTGGAAGCC
TTGGATG
Found at i:3772050 original size:207 final size:208
Alignment explanation
Indices: 3771636--3772059 Score: 760
Period size: 207 Copynumber: 2.0 Consensus size: 208
3771626 TAAAAGCTCT
* * *
3771636 ATCAATATCTCCTTTTGCTCACTCGGAGAAGATTCTCAGCTTAAGCATTTCCTCACATTGGCAGT
1 ATCAAAATCTCCTTTTGCTCACTCGGAGAAGACTCTCAACTTAAGCATTTCCTCACATTGGCAGT
* * *
3771701 TTTAGTTGTTCATGCAGGAACACCAAATTTTGTTTCATGCCCATAATATTTTAAATTTGACAAGC
66 TTTAGCTGTTCATACAGGAACACCAAATTTTGTTTCATGCCCAAAATATTTTAAATTTGACAAGC
*
3771766 AACAATCAAGAACATATTTATTCACAAAATGGTTAATGTAGCATTGAAATTTACAAATTCGGTGT
131 AACAATCAAGAACATATTTATTCACAAAATGGTTAATGTAACATTGAAATTTACAAATTCGGTGT
3771831 AATTTCATAAGGG
196 AATTTCATAAGGG
3771844 ATCAAAATCTCCTTTTGCTCACTCGGAGAAGACTCTCAACTTAAGCATTTCCTCACATTGGCAGT
1 ATCAAAATCTCCTTTTGCTCACTCGGAGAAGACTCTCAACTTAAGCATTTCCTCACATTGGCAGT
3771909 TTTAGCTGTTCATACAGGAACACCAAATTTTGTTTCATG-CCAAAATATTTTAAATTTGACAAGC
66 TTTAGCTGTTCATACAGGAACACCAAATTTTGTTTCATGCCCAAAATATTTTAAATTTGACAAGC
* *
3771973 AACAATCAAGAACATATTTATTCACAAAATGGTTGATGTAACATTGAAATTTACAAATTGGGTGT
131 AACAATCAAGAACATATTTATTCACAAAATGGTTAATGTAACATTGAAATTTACAAATTCGGTGT
3772038 AATTTCATAAGGG
196 AATTTCATAAGGG
3772051 ATCAAAATC
1 ATCAAAATC
3772060 ATGCAAGAAT
Statistics
Matches: 207, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
207 108 0.52
208 99 0.48
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (208 bp):
ATCAAAATCTCCTTTTGCTCACTCGGAGAAGACTCTCAACTTAAGCATTTCCTCACATTGGCAGT
TTTAGCTGTTCATACAGGAACACCAAATTTTGTTTCATGCCCAAAATATTTTAAATTTGACAAGC
AACAATCAAGAACATATTTATTCACAAAATGGTTAATGTAACATTGAAATTTACAAATTCGGTGT
AATTTCATAAGGG
Found at i:3773145 original size:22 final size:22
Alignment explanation
Indices: 3773113--3773162 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
3773103 AAAATTTTAA
3773113 ATTTAAATAAAAAATTATATTT
1 ATTTAAATAAAAAATTATATTT
* *
3773135 ATTTAATTAAAAACTTATATTT
1 ATTTAAATAAAAAATTATATTT
3773157 -TTTAAA
1 ATTTAAA
3773163 ATTTATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTAAATAAAAAATTATATTT
Found at i:3773146 original size:21 final size:22
Alignment explanation
Indices: 3773113--3773161 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
3773103 AAAATTTTAA
3773113 ATTTAAATAAAAAA-TTATATTT
1 ATTT-AATAAAAAACTTATATTT
*
3773135 ATTTAATTAAAAACTTATATTT
1 ATTTAATAAAAAACTTATATTT
3773157 -TTTAA
1 ATTTAA
3773162 AATTTATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAATAAAAAACTTATATTT
Found at i:3777048 original size:2 final size:2
Alignment explanation
Indices: 3777041--3777080 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
3777031 AATTTAACAA
3777041 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3777080 A
1 A
3777081 AACATTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3781168 original size:1 final size:1
Alignment explanation
Indices: 3781162--3781196 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
3781152 AGGTGTAGCT
3781162 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3781197 CAGGCAAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3789711 original size:29 final size:31
Alignment explanation
Indices: 3789666--3789724 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
3789656 TAATTTTTTA
*
3789666 ATTTTTAAAAGTTTAAAAATTA-TAAAATTT
1 ATTTTTAAAAGATTAAAAATTATTAAAATTT
3789696 ATTTTTAAAA-ATTAAAAATTATTAAAATT
1 ATTTTTAAAAGATTAAAAATTATTAAAATT
3789725 ATTAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (31 bp):
ATTTTTAAAAGATTAAAAATTATTAAAATTT
Found at i:3789732 original size:20 final size:21
Alignment explanation
Indices: 3789709--3789755 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3789699 TTTAAAAATT
*
3789709 AAAAAT-TATTAAAAT-TATTA
1 AAAAATGTATAAAAATAT-TTA
3789729 AAAAATGTATAAAAATATTTA
1 AAAAATGTATAAAAATATTTA
3789750 AAAAAT
1 AAAAAT
3789756 ATTTTTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
21 17 0.71
22 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAAATGTATAAAAATATTTA
Found at i:3789733 original size:21 final size:21
Alignment explanation
Indices: 3789709--3789773 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 21
3789699 TTTAAAAATT
3789709 AAAAATTATTAAAATTATT-A
1 AAAAATTATTAAAATTATTAA
*
3789729 AAAAATGTA-TAAAAATATTTAA
1 AAAAAT-TATTAAAATTA-TTAA
* *
3789751 AAAATATTTTTAATATT-TTAA
1 AAAA-ATTATTAAAATTATTAA
3789772 AA
1 AA
3789774 TGTAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
20 13 0.36
21 10 0.28
22 6 0.17
23 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAATTATTAAAATTATTAA
Found at i:3791041 original size:18 final size:17
Alignment explanation
Indices: 3791011--3791101 Score: 69
Period size: 17 Copynumber: 5.1 Consensus size: 17
3791001 TAGTAAAAAT
3791011 ATAATTTTATTATTTTA
1 ATAATTTTATTATTTTA
3791028 ATAATTTATATTATTTTA
1 ATAATTT-TATTATTTTA
* * *
3791046 AT--TTTTAAATAGTTAA
1 ATAATTTT-ATTATTTTA
*
3791062 ATTAAATTTTTATTATTTTT
1 A-T-AA-TTTTATTATTTTA
*
3791082 TTAATTTTATTATTATTA
1 ATAATTTTATTATT-TTA
3791100 AT
1 AT
3791102 TTAAAATTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
15 1 0.02
16 10 0.18
17 18 0.32
18 17 0.30
19 1 0.02
20 5 0.09
21 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (17 bp):
ATAATTTTATTATTTTA
Found at i:3791106 original size:39 final size:39
Alignment explanation
Indices: 3791032--3791120 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
3791022 ATTTTAATAA
*
3791032 TTTA-TATTATTTTAATTTTTAAATAGTTAAATTAAATT
1 TTTATTATTATTTTAATTTTTAAATAGTTAAATTAAAAT
* * * *
3791070 TTTATTATTTTTTTAATTTTATTATTA-TTAATTTAAAAT
1 TTTATTATTATTTTAATTTT-TAAATAGTTAAATTAAAAT
3791109 TTTATATATTAT
1 TTTAT-TATTAT
3791121 AATGGGCTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
38 4 0.10
39 29 0.69
40 9 0.21
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (39 bp):
TTTATTATTATTTTAATTTTTAAATAGTTAAATTAAAAT
Found at i:3795154 original size:32 final size:34
Alignment explanation
Indices: 3795118--3795186 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
3795108 TATTACATTA
*
3795118 AAAAATAGGT-AAAAATTAC-AGGAAA-AAAATCC
1 AAAAATAGGTGAAAAACTACAAGGAAAGAAAA-CC
*
3795150 AAAAATAGGTGAAAACCTACAAGGAAAGAAAACC
1 AAAAATAGGTGAAAAACTACAAGGAAAGAAAACC
3795184 AAA
1 AAA
3795187 GGGATGTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 7 0.22
34 11 0.34
35 4 0.12
ACGTcount: A:0.62, C:0.12, G:0.14, T:0.12
Consensus pattern (34 bp):
AAAAATAGGTGAAAAACTACAAGGAAAGAAAACC
Found at i:3798922 original size:21 final size:21
Alignment explanation
Indices: 3798896--3798935 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3798886 GAATTCAAAC
3798896 TCTAAACCTCAAACTTAAAAT
1 TCTAAACCTCAAACTTAAAAT
*
3798917 TCTAAACCTCAAATTTAAA
1 TCTAAACCTCAAACTTAAA
3798936 CCCTAAATTT
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:0.23, G:0.00, T:0.30
Consensus pattern (21 bp):
TCTAAACCTCAAACTTAAAAT
Found at i:3805796 original size:81 final size:81
Alignment explanation
Indices: 3805473--3805897 Score: 566
Period size: 81 Copynumber: 5.2 Consensus size: 81
3805463 AAGGTAACTT
*
3805473 TTTTAACCCCTGGATGAATACGAGTTATATGTCGAAAACATTAAGAATCCTGTCCTGTATGATAC
1 TTTTAACCCTTGGATGAATACGAGTTATATGTCGAAAACATTAAGAATCCTGTCCTGTATGATAC
* *
3805538 TATTTTGAAATGGATC
66 TAGTTTGTAATGGATC
** * * * * *
3805554 TTTTAA-TTTTGGATGAATATGAGTTATATGCCGATAACGTTAAGAATCCTGACCTGTATGATAC
1 TTTTAACCCTTGGATGAATACGAGTTATATGTCGAAAACATTAAGAATCCTGTCCTGTATGATAC
*
3805618 TAGTTTGTAACGGATC
66 TAGTTTGTAATGGATC
*
3805634 TTTTAACCCTTGGATGAGTAC-AGGTTATATGTCGAAAAACATTAAGAATCCTGTCCTGTATGAT
1 TTTTAACCCTTGGATGAATACGA-GTTATATGTCG-AAAACATTAAGAATCCTGTCCTGTATGAT
3805698 ACTAGTTTGTAATGGATC
64 ACTAGTTTGTAATGGATC
* * * *
3805716 TTTTAACTCTTGGATGAGTACAAGTTATATGTCGAAAACATTAAGAATCCTGACCTGTATGATAC
1 TTTTAACCCTTGGATGAATACGAGTTATATGTCGAAAACATTAAGAATCCTGTCCTGTATGATAC
* * *
3805781 TCGTTTGTTACGGATC
66 TAGTTTGTAATGGATC
* * * *
3805797 TTTTAACCCTTGGATGAATATGAGTTATATGCCGATAACGTTAAGAATCCTGTCCTGTATGATAC
1 TTTTAACCCTTGGATGAATACGAGTTATATGTCGAAAACATTAAGAATCCTGTCCTGTATGATAC
* * **
3805862 TAGTTCGTTATGCTTC
66 TAGTTTGTAATGGATC
*
3805878 TTTTATCCCTTGGATGAATA
1 TTTTAACCCTTGGATGAATA
3805898 TATATTGAAG
Statistics
Matches: 301, Mismatches: 39, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
80 70 0.23
81 156 0.52
82 74 0.25
83 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (81 bp):
TTTTAACCCTTGGATGAATACGAGTTATATGTCGAAAACATTAAGAATCCTGTCCTGTATGATAC
TAGTTTGTAATGGATC
Found at i:3808313 original size:22 final size:22
Alignment explanation
Indices: 3808287--3808328 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3808277 TATATTGAAA
**
3808287 ATTAGATAAATTTAATTATTCT
1 ATTAGATAAATGAAATTATTCT
*
3808309 ATTAGGTAAATGAAATTATT
1 ATTAGATAAATGAAATTATT
3808329 TTTATATGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (22 bp):
ATTAGATAAATGAAATTATTCT
Found at i:3817575 original size:2 final size:2
Alignment explanation
Indices: 3817570--3817595 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3817560 CTACTGTTCA
3817570 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3817596 GGAAACAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3827202 original size:16 final size:15
Alignment explanation
Indices: 3827181--3827214 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3827171 ATGCAAACAT
3827181 AATAATTTAAATATAA
1 AATAA-TTAAATATAA
*
3827197 AATAATTCAATATAA
1 AATAATTAAATATAA
3827212 AAT
1 AAT
3827215 TTGATAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATTAAATATAA
Found at i:3827955 original size:16 final size:16
Alignment explanation
Indices: 3827931--3827965 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3827921 TTAAAAAGGA
* *
3827931 AAACTCAAATTAATTT
1 AAACACAAAATAATTT
3827947 AAACACAAAATAATTT
1 AAACACAAAATAATTT
3827963 AAA
1 AAA
3827966 ATTTCTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (16 bp):
AAACACAAAATAATTT
Found at i:3829275 original size:2 final size:2
Alignment explanation
Indices: 3829262--3829294 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3829252 TGGGTGTCTA
*
3829262 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3829295 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3829299 original size:2 final size:2
Alignment explanation
Indices: 3829294--3829345 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3829284 ATATATATAT
3829294 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3829336 AG AG AG AG AG
1 AG AG AG AG AG
3829346 CTTATATGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3838881 original size:25 final size:25
Alignment explanation
Indices: 3838843--3838899 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
3838833 CCAGCAGTGA
* *
3838843 CACCACCAGCTTCAACTTGCTCTGC
1 CACCACCAACTTCAACCTGCTCTGC
* *
3838868 CACCACCAATTTCAACCTGTTCTGC
1 CACCACCAACTTCAACCTGCTCTGC
*
3838893 CATCACC
1 CACCACC
3838900 GCCACTGCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.44, G:0.09, T:0.25
Consensus pattern (25 bp):
CACCACCAACTTCAACCTGCTCTGC
Found at i:3839408 original size:13 final size:13
Alignment explanation
Indices: 3839387--3839419 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3839377 ATAATAACAT
3839387 TTAAT-AATAATA
1 TTAATAAATAATA
3839399 TTAATAAATAATA
1 TTAATAAATAATA
*
3839412 ATAATAAA
1 TTAATAAA
3839420 CAAGAGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAATAAATAATA
Found at i:3844228 original size:22 final size:22
Alignment explanation
Indices: 3844203--3844245 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3844193 AGATACCATA
3844203 AATACTAACT-TTTAAATATAAT
1 AATACTAA-TATTTAAATATAAT
* *
3844225 AATATTAATATTTTAATATAA
1 AATACTAATATTTAAATATAA
3844246 AATTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (22 bp):
AATACTAATATTTAAATATAAT
Found at i:3844256 original size:19 final size:23
Alignment explanation
Indices: 3844212--3844257 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
3844202 AAATACTAAC
3844212 TTTTAAATATAATAATATTAATA
1 TTTTAAATATAATAATATTAATA
3844235 TTTT-AATATAA-AAT-TTAA-A
1 TTTTAAATATAATAATATTAATA
3844254 TTTT
1 TTTT
3844258 GTAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 4 0.17
21 3 0.13
22 7 0.30
23 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTAAATATAATAATATTAATA
Found at i:3846594 original size:20 final size:22
Alignment explanation
Indices: 3846571--3846610 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
3846561 AATCAAATCA
*
3846571 TGAACAGTAA-AAT-TATATCG
1 TGAACAATAATAATATATATCG
3846591 TGAACAATAATAATATATAT
1 TGAACAATAATAATATATAT
3846611 ATAAATATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (22 bp):
TGAACAATAATAATATATATCG
Found at i:3867878 original size:16 final size:16
Alignment explanation
Indices: 3867857--3867890 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3867847 ACCAGTATCA
*
3867857 CACTCTTTGAATAGGT
1 CACTCTTTAAATAGGT
*
3867873 CACTCTTTAAATTGGT
1 CACTCTTTAAATAGGT
3867889 CA
1 CA
3867891 ATACCTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (16 bp):
CACTCTTTAAATAGGT
Found at i:3884986 original size:22 final size:20
Alignment explanation
Indices: 3884939--3884986 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
3884929 TGTTTGTCTC
3884939 AGGTTATATTTTAGTCATTT
1 AGGTTATATTTTAGTCATTT
* *
3884959 ACGTTATCATTTTATTACATTT
1 AGGTTAT-ATTTTAGT-CATTT
*
3884981 TGGTTA
1 AGGTTA
3884987 CTGAGTTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.54
Consensus pattern (20 bp):
AGGTTATATTTTAGTCATTT
Found at i:3887738 original size:27 final size:26
Alignment explanation
Indices: 3887708--3887778 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
3887698 GTTTTTTGTG
*
3887708 TTTTTTTTATAATTTTGA-TTTTAAT
1 TTTTTTTTATAATTTTAATTTTTAAT
**
3887733 GATTTTTTTTACTCTTTTATAATTTTTAAT
1 --TTTTTTTTA-TAATTT-TAATTTTTAAT
3887763 TTTTTTTTATAATTTT
1 TTTTTTTTATAATTTT
3887779 TAGTATGCTC
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
26 1 0.03
27 13 0.36
28 13 0.36
29 2 0.06
30 7 0.19
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (26 bp):
TTTTTTTTATAATTTTAATTTTTAAT
Found at i:3887850 original size:18 final size:19
Alignment explanation
Indices: 3887810--3887852 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3887800 GCATGTTTTC
3887810 AAAATTAAGTTTTGAGATG
1 AAAATTAAGTTTTGAGATG
* *
3887829 AAAATTAATTTTTGATAT-
1 AAAATTAAGTTTTGAGATG
3887847 AAAATT
1 AAAATT
3887853 TTTTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (19 bp):
AAAATTAAGTTTTGAGATG
Found at i:3887870 original size:21 final size:21
Alignment explanation
Indices: 3887844--3887885 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3887834 TAATTTTTGA
* *
3887844 TATAAAATTTTTTTTTATACT
1 TATAAAATTTTTATATATACT
3887865 TATAAAATTTTTATATATACT
1 TATAAAATTTTTATATATACT
3887886 ATTAATTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TATAAAATTTTTATATATACT
Found at i:3896947 original size:126 final size:126
Alignment explanation
Indices: 3896722--3896976 Score: 438
Period size: 126 Copynumber: 2.0 Consensus size: 126
3896712 ATGAGATGTT
* * *
3896722 GAAGAACACTCTGACTAACCGAGGATAACAAGCACGATGCAAGAGCACTATGTTGCTGCTCAAAA
1 GAAGAACACTCTGACTAACCGAGGATAACAACCACGATGCAAGAGCACTATCTTACTGCTCAAAA
*
3896787 CGCTCAAACTCATGGTTTTCTTAAGAGCTTCCATTTTCTCCAATAACAAGTCGAGAAGGAG
66 CGCTCAAACTCAGGGTTTTCTTAAGAGCTTCCATTTTCTCCAATAACAAGTCGAGAAGGAG
* *
3896848 GAAGAACACTCTGACTAATCGAGGATAACAACCACGATGCAAGAGCACTATCTTACTGTTCAAAA
1 GAAGAACACTCTGACTAACCGAGGATAACAACCACGATGCAAGAGCACTATCTTACTGCTCAAAA
* *
3896913 CGCTCAAACTCAGGGTTTTCTTGAGAGCTTCCATTTTCTCCAGTAACAAGTCGAGAAGGAG
66 CGCTCAAACTCAGGGTTTTCTTAAGAGCTTCCATTTTCTCCAATAACAAGTCGAGAAGGAG
3896974 GAA
1 GAA
3896977 CAGTATCTGA
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 121 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (126 bp):
GAAGAACACTCTGACTAACCGAGGATAACAACCACGATGCAAGAGCACTATCTTACTGCTCAAAA
CGCTCAAACTCAGGGTTTTCTTAAGAGCTTCCATTTTCTCCAATAACAAGTCGAGAAGGAG
Found at i:3909786 original size:20 final size:20
Alignment explanation
Indices: 3909761--3909798 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3909751 AAAATAAAAT
*
3909761 ATTTTATTAAATATTTATAA
1 ATTTTAATAAATATTTATAA
*
3909781 ATTTTAATATATATTTAT
1 ATTTTAATAAATATTTAT
3909799 TATTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTAATAAATATTTATAA
Found at i:3909926 original size:16 final size:17
Alignment explanation
Indices: 3909882--3909942 Score: 51
Period size: 18 Copynumber: 3.7 Consensus size: 17
3909872 TTAAAGTTTA
3909882 TTATTAA-AATAA-AA-
1 TTATTAATAATAATAAT
*
3909896 TT-TTAATATTAAATAAT
1 TTATTAATAAT-AATAAT
3909913 TTATTAA-AATAATAAAT
1 TTATTAATAATAAT-AAT
3909930 TATATTAATAATA
1 T-TATTAATAATA
3909943 TTATTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
13 4 0.11
14 4 0.11
15 2 0.05
16 5 0.14
17 8 0.22
18 10 0.27
19 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATTAATAATAATAAT
Found at i:3909937 original size:30 final size:31
Alignment explanation
Indices: 3909834--3909950 Score: 98
Period size: 31 Copynumber: 3.6 Consensus size: 31
3909824 TTTCAGTAAT
3909834 ATATTAATAATATTATTAAAAATTTAAAATTATTA
1 ATATTAATAATATTATT-AAAA--TAAAA-TATTA
* * * *
3909869 TTCTTAA-AGTTTATTATTAAAATAAAATTTTA
1 ATATTAATA--ATATTATTAAAATAAAATATTA
3909901 ATATTAAATAAT-TTATTAAAATAATAA-ATT-
1 ATATT-AATAATATTATTAAAATAA-AATATTA
3909931 ATATTAATAATATTATTAAA
1 ATATTAATAATATTATTAAA
3909951 TTATTGAATA
Statistics
Matches: 68, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
29 6 0.09
30 13 0.19
31 14 0.21
32 10 0.15
33 7 0.10
34 2 0.03
35 9 0.13
36 7 0.10
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
ATATTAATAATATTATTAAAATAAAATATTA
Found at i:3909970 original size:22 final size:22
Alignment explanation
Indices: 3909917--3909973 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3909907 AATAATTTAT
*
3909917 TAAAATAA-TAAATTATATTAA
1 TAAAATAATTAAATTATATGAA
* *
3909938 TAATATTATTAAATTAT-TGAA
1 TAAAATAATTAAATTATATGAA
3909959 TATAAATAATTAAAT
1 TA-AAATAATTAAAT
3909974 ACATATGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAAATAATTAAATTATATGAA
Found at i:3911581 original size:21 final size:21
Alignment explanation
Indices: 3911564--3911610 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3911554 GAATAAACCA
*
3911564 TAAACCTTAAACCTTAAACTC
1 TAAACCTCAAACCTTAAACTC
* *
3911585 TAAACCTCAAACTTTAAACTT
1 TAAACCTCAAACCTTAAACTC
3911606 TAAAC
1 TAAAC
3911611 TTGAACCCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAACCTCAAACCTTAAACTC
Found at i:3911611 original size:14 final size:14
Alignment explanation
Indices: 3911557--3911612 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
3911547 GAAACTTGAA
* *
3911557 TAAACCATAAACCT
1 TAAACCTTAAACTT
*
3911571 TAAACCTTAAACTC
1 TAAACCTTAAACTT
*
3911585 TAAACCTCAAACTT
1 TAAACCTTAAACTT
*
3911599 TAAACTTTAAACTT
1 TAAACCTTAAACTT
3911613 GAACCCTGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAACCTTAAACTT
Found at i:3911612 original size:7 final size:7
Alignment explanation
Indices: 3911564--3911612 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
3911554 GAATAAACCA
*
3911564 TAAACCT
1 TAAACTT
*
3911571 TAAACCT
1 TAAACTT
*
3911578 TAAACTC
1 TAAACTT
*
3911585 TAAACCT
1 TAAACTT
*
3911592 CAAACTT
1 TAAACTT
3911599 TAAACTT
1 TAAACTT
3911606 TAAACTT
1 TAAACTT
3911613 GAACCCTGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (7 bp):
TAAACTT
Found at i:3911649 original size:14 final size:14
Alignment explanation
Indices: 3911572--3911649 Score: 52
Period size: 14 Copynumber: 5.7 Consensus size: 14
3911562 CATAAACCTT
* *
3911572 AAACCTTAAACTCT
1 AAACCTCAAACTCG
**
3911586 AAACCTCAAACTTT
1 AAACCTCAAACTCG
* * *
3911600 AAACTTTAAACTTG
1 AAACCTCAAACTCG
* * *
3911614 AACCCTGAACCTC-
1 AAACCTCAAACTCG
3911627 AAA-CTCAAACTCG
1 AAACCTCAAACTCG
3911640 AAACCTCAAA
1 AAACCTCAAA
3911650 ATATTCAAGG
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
12 7 0.14
13 5 0.10
14 37 0.76
ACGTcount: A:0.44, C:0.29, G:0.04, T:0.23
Consensus pattern (14 bp):
AAACCTCAAACTCG
Found at i:3911699 original size:13 final size:13
Alignment explanation
Indices: 3911681--3911710 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3911671 AGTTTAGGGC
3911681 TTAAGATTCGAGT
1 TTAAGATTCGAGT
*
3911694 TTAAGATTTGAGT
1 TTAAGATTCGAGT
3911707 TTAA
1 TTAA
3911711 TTTGAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.43
Consensus pattern (13 bp):
TTAAGATTCGAGT
Found at i:3918058 original size:24 final size:23
Alignment explanation
Indices: 3917981--3918067 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
3917971 TAATGTTCAC
* *
3917981 GAACATGTTCATTTAGC-TTAATT
1 GAACATGTTCA-TGAACATTAATT
* * * *
3918004 GTATATGTTCACGAACATTAAAT
1 GAACATGTTCATGAACATTAATT
3918027 GAACATGTTCATGAACATATAATT
1 GAACATGTTCATGAACAT-TAATT
*
3918051 GAACATGTTCATAAACA
1 GAACATGTTCATGAACA
3918068 ATGTTAAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
22 2 0.04
23 29 0.57
24 20 0.39
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (23 bp):
GAACATGTTCATGAACATTAATT
Found at i:3918111 original size:4 final size:4
Alignment explanation
Indices: 3918104--3918140 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
3918094 CAAACAATAT
3918104 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
3918141 CACACATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:3923201 original size:59 final size:57
Alignment explanation
Indices: 3923078--3923217 Score: 156
Period size: 59 Copynumber: 2.4 Consensus size: 57
3923068 TATGGATACC
* *
3923078 CGGGGGCAAAATAGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAGGTTT
1 CGGGGGTAAAAT-GTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAGATTT
* * * *
3923136 CGGGGGTAAAATGGTAAATTTTGGTGAAATTGGGGTTAAAAATGGGA-TTTAGGAGATTTT
1 CGGGGGTAAAAT-GT-AATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTA-AAGA-TTT
* *
3923196 TGGGGTTAAAATGTAATTTTGG
1 CGGGGGTAAAATGTAATTTTGG
3923218 AAAAGTTTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
58 25 0.36
59 32 0.46
60 13 0.19
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.34
Consensus pattern (57 bp):
CGGGGGTAAAATGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAGATTT
Found at i:3923227 original size:30 final size:30
Alignment explanation
Indices: 3923193--3923393 Score: 305
Period size: 30 Copynumber: 6.7 Consensus size: 30
3923183 TTTAGGAGAT
*
3923193 TTTTGGGGTTAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
*
3923223 TTTTGGGGTCAAAATGTAATTTTAGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
3923253 TTTTGGGGTCAAAATGTAATTTTGGAAAA-
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
* * *
3923282 TTTTAGGGTTAAAATGTAATTTTGAAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
*
3923312 TTTTGGGGTCAAAATATAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
* * * *
3923342 TTTTAGGGTTAAAATATAATTTTGGAAAGG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
3923372 TTTTGGGGTCAAAATGTAATTT
1 TTTTGGGGTCAAAATGTAATTT
3923394 CTAGATTGTT
Statistics
Matches: 154, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
29 26 0.17
30 128 0.83
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.39
Consensus pattern (30 bp):
TTTTGGGGTCAAAATGTAATTTTGGAAAAG
Found at i:3923267 original size:89 final size:89
Alignment explanation
Indices: 3923165--3923393 Score: 305
Period size: 89 Copynumber: 2.6 Consensus size: 89
3923155 TTTGGTGAAA
** * * * *
3923165 TTGGGGTTAAAAATGGGATTTAGGAGATTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTGGG
1 TTGGGG-TAAAAATGTAATTTTGGAAAATTTTGGGGTTAAAATGTAATTTTGAAAAAGTTTTGGG
*
3923230 GTCAAAATGTAATTTTAGAAAAGTT
65 GTCAAAATATAATTTTAGAAAAGTT
* *
3923255 TTGGGGTCAAAATGTAATTTTGGAAAATTTTAGGGTTAAAATGTAATTTTGAAAAAGTTTTGGGG
1 TTGGGGTAAAAATGTAATTTTGGAAAATTTTGGGGTTAAAATGTAATTTTGAAAAAGTTTTGGGG
*
3923320 TCAAAATATAATTTTGGAAAAGTT
66 TCAAAATATAATTTTAGAAAAGTT
* * * * *
3923344 TTAGGGTTAAAATATAATTTTGGAAAGGTTTTGGGGTCAAAATGTAATTT
1 TTGGGGTAAAAATGTAATTTTGGAAA-ATTTTGGGGTTAAAATGTAATTT
3923394 CTAGATTGTT
Statistics
Matches: 122, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
89 96 0.79
90 26 0.21
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (89 bp):
TTGGGGTAAAAATGTAATTTTGGAAAATTTTGGGGTTAAAATGTAATTTTGAAAAAGTTTTGGGG
TCAAAATATAATTTTAGAAAAGTT
Found at i:3924458 original size:3 final size:3
Alignment explanation
Indices: 3924450--3924482 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3924440 GTCCTTTCAG
*
3924450 TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3924483 ATGTCTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3925170 original size:17 final size:16
Alignment explanation
Indices: 3925143--3925222 Score: 79
Period size: 17 Copynumber: 4.7 Consensus size: 16
3925133 TTATGATAAT
3925143 ATTAAATTTTAAATTAA
1 ATTAAA-TTTAAATTAA
3925160 ATTCAAATTTAAATTTAA
1 ATT-AAATTTAAA-TTAA
* *
3925178 ATTTAAATTGAATTTAA
1 A-TTAAATTTAAATTAA
*
3925195 AGTAAATTTAAGATTAA
1 ATTAAATTTAA-ATTAA
*
3925212 AATAAATTTAA
1 ATTAAATTTAA
3925223 TTTTCAAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.15
17 28 0.53
18 15 0.28
19 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTAAATTTAAATTAA
Found at i:3925173 original size:6 final size:6
Alignment explanation
Indices: 3925144--3925222 Score: 69
Period size: 6 Copynumber: 13.7 Consensus size: 6
3925134 TATGATAATA
* *
3925144 TTAAATT TTAAA- TTAAAT TCAAAT TTAAAT TTAAAT TTAAA- TTGAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
3925191 TTAAA- GTAAAT TTAAGA- TTAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAA
3925223 TTTTCAAATG
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
5 18 0.31
6 35 0.59
7 6 0.10
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:3925193 original size:11 final size:11
Alignment explanation
Indices: 3925151--3925225 Score: 73
Period size: 11 Copynumber: 6.7 Consensus size: 11
3925141 ATATTAAATT
3925151 TTAAA-TTAAA
1 TTAAATTTAAA
3925161 TTCAAATTTAAA
1 TT-AAATTTAAA
3925173 TTTAAATTTAAA
1 -TTAAATTTAAA
*
3925185 TTGAATTTAAA
1 TTAAATTTAAA
*
3925196 GTAAATTTAAGA
1 TTAAATTTAA-A
*
3925208 TTAAA-ATAAA
1 TTAAATTTAAA
*
3925218 TTTAATTT
1 TTAAATTT
3925226 TCAAATGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
10 7 0.13
11 25 0.47
12 19 0.36
13 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:3925599 original size:68 final size:68
Alignment explanation
Indices: 3925515--3925884 Score: 623
Period size: 68 Copynumber: 5.4 Consensus size: 68
3925505 AAGACTTTGC
* * *
3925515 TATCCAACTTTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAAAC
1 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
*
3925580 GTGT
65 ATGT
* * *
3925584 TATCCAATCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTTAGAGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
3925649 TGT
66 TGT
*
3925652 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
3925717 TGT
66 TGT
* * * *
3925720 TATCCATTTTACTTAAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGCGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
3925785 TGT
66 TGT
3925788 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
3925853 TGT
66 TGT
3925856 TATCCACTCTACTTCAATTTCAAGGGGAT
1 TATCCACTCTACTTCAATTTCAAGGGGAT
3925885 AGGAAAAGGT
Statistics
Matches: 283, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
68 278 0.98
69 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (68 bp):
TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
TGT
Found at i:3925741 original size:37 final size:36
Alignment explanation
Indices: 3925555--3925877 Score: 182
Period size: 37 Copynumber: 9.4 Consensus size: 36
3925545 GACGTTGCTC
* *
3925555 TTACTTCAATTTCAGAGATGAAAACGTGTTATCCAAT
1 TTACTTCAATTTCAGAGATGAAGAC-TGTTATCCATT
* * * * *
3925592 CTACTTCAATTTCA-AGAGGATGAC-G-T-TGC-TC
1 TTACTTCAATTTCAGAGATGAAGACTGTTATCCATT
* *
3925623 TTACTTCAATTTTAGAGATGAAGACATGTTATCCACT
1 TTACTTCAATTTCAGAGATGAAGAC-TGTTATCCATT
* ** * * *
3925660 CTACTTCAATTTCA-AGGGGATGAC-G-T-TGC-TC
1 TTACTTCAATTTCAGAGATGAAGACTGTTATCCATT
3925691 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCATT
1 TTACTTCAATTTCAGAGATGAAGAC-TGTTATCCATT
* ** * * *
3925728 TTACTTAAATTTCA-AGGGGATGAC-G-T-TGC-TC
1 TTACTTCAATTTCAGAGATGAAGACTGTTATCCATT
* *
3925759 TTACTTCAATTTCAGCGATGAAGACATGTTATCCACT
1 TTACTTCAATTTCAGAGATGAAGAC-TGTTATCCATT
* ** * * *
3925796 CTACTTCAATTTCA-AGGGGATGAC-G-T-TGC-TC
1 TTACTTCAATTTCAGAGATGAAGACTGTTATCCATT
*
3925827 TTACTTCAATTTCAGAGATGAAGACATGTTATCCACT
1 TTACTTCAATTTCAGAGATGAAGAC-TGTTATCCATT
*
3925864 CTACTTCAATTTCA
1 TTACTTCAATTTCA
3925878 AGGGGATAGG
Statistics
Matches: 204, Mismatches: 58, Indels: 48
0.66 0.19 0.15
Matches are distributed among these distances:
31 52 0.25
32 36 0.18
33 4 0.02
34 8 0.04
35 4 0.02
36 35 0.17
37 65 0.32
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (36 bp):
TTACTTCAATTTCAGAGATGAAGACTGTTATCCATT
Found at i:3930137 original size:18 final size:18
Alignment explanation
Indices: 3930114--3930149 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3930104 TATATTACAA
3930114 TCCTGGTCATCTTCAAAG
1 TCCTGGTCATCTTCAAAG
3930132 TCCTGGTCATCTTCAAAG
1 TCCTGGTCATCTTCAAAG
3930150 ATCTGTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (18 bp):
TCCTGGTCATCTTCAAAG
Found at i:3938020 original size:59 final size:58
Alignment explanation
Indices: 3937892--3938030 Score: 160
Period size: 58 Copynumber: 2.4 Consensus size: 58
3937882 TATGGATACC
*
3937892 CGGGGG-CAAAATAGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAGGTTT
1 CGGGGGTCAAAAT-GTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAGATTT
* * *
3937950 CGGGGGT-AAAATGGTAAATTTTGGTGAAATCGGGGTT-AAAATGGGA-TTTAGGAGATTT
1 CGGGGGTCAAAAT-GT-AATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTA-AAGATTT
**
3938008 TTGGGGTCAAAATGTAATTTTGG
1 CGGGGGTCAAAATGTAATTTTGG
3938031 GGTTAAAATG
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
57 12 0.17
58 33 0.47
59 25 0.36
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.32
Consensus pattern (58 bp):
CGGGGGTCAAAATGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAGATTT
Found at i:3938030 original size:19 final size:19
Alignment explanation
Indices: 3938006--3938079 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
3937996 TTTAGGAGAT
3938006 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
*
3938025 TTTTGGGGTTAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
3938044 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
3938055 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
3938074 TTTTGG
1 TTTTGG
3938080 AAAAGTTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
11 4 0.09
13 2 0.04
14 1 0.02
15 8 0.17
16 1 0.02
17 2 0.04
19 28 0.61
ACGTcount: A:0.30, C:0.03, G:0.27, T:0.41
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:3938061 original size:30 final size:30
Alignment explanation
Indices: 3938025--3938137 Score: 208
Period size: 30 Copynumber: 3.8 Consensus size: 30
3938015 CAAAATGTAA
*
3938025 TTTTGGGGTTAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
3938055 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
*
3938085 TTTTGGGGTCAAAATATAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
3938115 TTTTGGGGTCAAAATGTAATTTT
1 TTTTGGGGTCAAAATGTAATTTT
3938138 TAGATTGTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.40
Consensus pattern (30 bp):
TTTTGGGGTCAAAATGTAATTTTGGAAAAG
Found at i:3939215 original size:3 final size:3
Alignment explanation
Indices: 3939207--3939242 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3939197 TCCTTTCGGT
*
3939207 TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3939243 ATGTCTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3939932 original size:17 final size:16
Alignment explanation
Indices: 3939905--3939981 Score: 66
Period size: 17 Copynumber: 4.6 Consensus size: 16
3939895 TTATGATAAT
3939905 ATTAAATTTTAAATTAA
1 ATTAAA-TTTAAATTAA
3939922 ATTCAAATTTAAATTTAA
1 ATT-AAATTTAAA-TTAA
* *
3939940 ATTGAATTTAAAGTAA
1 ATTAAATTTAAATTAA
*
3939956 ATTTAAGA-TTAAAATAA
1 A-TTAA-ATTTAAATTAA
*
3939973 ATTTAATTT
1 ATTAAATTT
3939982 TCAAATGGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
15 1 0.02
16 9 0.18
17 29 0.58
18 11 0.22
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (16 bp):
ATTAAATTTAAATTAA
Found at i:3939935 original size:6 final size:6
Alignment explanation
Indices: 3939906--3939978 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
3939896 TATGATAATA
* *
3939906 TTAAATT TTAAA- TTAAAT TCAAAT TTAAAT TTAAA- TTGAAT TTAAA-
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
3939952 GTAAAT TTAAGA- TTAAA- ATAAAT TTAA
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAA
3939979 TTTTCAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
5 18 0.34
6 29 0.55
7 6 0.11
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:3939947 original size:11 final size:11
Alignment explanation
Indices: 3939905--3939981 Score: 75
Period size: 11 Copynumber: 6.8 Consensus size: 11
3939895 TTATGATAAT
3939905 ATTAAATTTTAA
1 ATTAAA-TTTAA
*
3939917 ATTAAATTCAA
1 ATTAAATTTAA
3939928 ATTTAAATTTAA
1 A-TTAAATTTAA
*
3939940 ATTGAATTTAA
1 ATTAAATTTAA
*
3939951 AGTAAATTTAA
1 ATTAAATTTAA
*
3939962 GATTAAA-ATAA
1 -ATTAAATTTAA
*
3939973 ATTTAATTT
1 ATTAAATTT
3939982 TCAAATGGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.09
11 27 0.51
12 21 0.40
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:3945287 original size:15 final size:15
Alignment explanation
Indices: 3945252--3945296 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
3945242 CTTAATTTTT
*
3945252 ATTTTTTTATAATTTTG
1 ATTTTTTTA-AA-TTTA
3945269 ATTTTTTTAAATTTA
1 ATTTTTTTAAATTTA
3945284 A-TTTTTTAAATTT
1 ATTTTTTTAAATTT
3945297 TTAAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 12 0.44
15 4 0.15
16 2 0.07
17 9 0.33
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
ATTTTTTTAAATTTA
Found at i:3945299 original size:16 final size:16
Alignment explanation
Indices: 3945245--3945300 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 16
3945235 AAAAACACTT
*
3945245 AATTTTTATTTTTTTA
1 AATTTTTAATTTTTTA
* *
3945261 TAATTTTGATTTTTTTA
1 -AATTTTTAATTTTTTA
3945278 AA--TTTAATTTTTTA
1 AATTTTTAATTTTTTA
3945292 AATTTTTAA
1 AATTTTTAA
3945301 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 12 0.35
16 7 0.21
17 15 0.44
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
AATTTTTAATTTTTTA
Found at i:3948554 original size:28 final size:29
Alignment explanation
Indices: 3948511--3948575 Score: 116
Period size: 28 Copynumber: 2.3 Consensus size: 29
3948501 CTAAATGCTA
3948511 CTAACTAACCAGCTAACTGCTAACTGACT
1 CTAACTAACCAGCTAACTGCTAACTGACT
3948540 CTAAC-AACCAGCTAACTGCTAACTGACT
1 CTAACTAACCAGCTAACTGCTAACTGACT
3948568 -TAACTAAC
1 CTAACTAAC
3948576 AAAGGTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 4 0.11
28 26 0.74
29 5 0.14
ACGTcount: A:0.37, C:0.31, G:0.09, T:0.23
Consensus pattern (29 bp):
CTAACTAACCAGCTAACTGCTAACTGACT
Found at i:3952215 original size:6 final size:7
Alignment explanation
Indices: 3952187--3952214 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3952177 CTCTCTCTAC
3952187 TCTTTTT
1 TCTTTTT
3952194 TCTTTTT
1 TCTTTTT
3952201 TCTTTTT
1 TCTTTTT
3952208 TCTTTTT
1 TCTTTTT
3952215 CCTGTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TCTTTTT
Found at i:3952937 original size:30 final size:31
Alignment explanation
Indices: 3952886--3952959 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
3952876 TAAGAAGTCT
3952886 AAATTTTTTTTACCAACTTTTAAA-AGATTTA
1 AAATTTTTTTTACCAACTTTTAAAGA-ATTTA
* *
3952917 AAATTTTTTTT-CTAATTTTTAAAGAATTTA
1 AAATTTTTTTTACCAACTTTTAAAGAATTTA
*
3952947 AAACTTTATTTTA
1 AAA-TTTTTTTTA
3952960 TTGTTTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 18 0.49
31 19 0.51
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (31 bp):
AAATTTTTTTTACCAACTTTTAAAGAATTTA
Found at i:3953473 original size:19 final size:20
Alignment explanation
Indices: 3953432--3953487 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 20
3953422 GCATGTTTTC
* * *
3953432 AAAATTAAGTTTTGAGATGA
1 AAAATTAATTTTTTATATGA
3953452 AAAATTAATTTTTTATAT-A
1 AAAATTAATTTTTTATATGA
* * *
3953471 AAATTTTATCTTTTATA
1 AAAATTAATTTTTTATA
3953488 CTTATAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (20 bp):
AAAATTAATTTTTTATATGA
Found at i:3956993 original size:37 final size:37
Alignment explanation
Indices: 3956901--3956994 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
3956891 TACATGTAAG
* * **
3956901 GTTAGTTGTCCGAGCTAAAATTATAAAATGACATCAA
1 GTTACTTGTCCGAGCTAAACTTATAAAACAACATCAA
** *
3956938 GTTACTCATCTGAGCTAAACTTATAAAACAACATCAA
1 GTTACTTGTCCGAGCTAAACTTATAAAACAACATCAA
*
3956975 GTTACTTGTCCGAACTAAAC
1 GTTACTTGTCCGAGCTAAAC
3956995 ATCTGTCACA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (37 bp):
GTTACTTGTCCGAGCTAAACTTATAAAACAACATCAA
Found at i:3959158 original size:21 final size:21
Alignment explanation
Indices: 3959143--3959181 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3959133 ATTTAATTAA
*
3959143 TATTTTTACAATTTTAAAAAT
1 TATTTTTAAAATTTTAAAAAT
3959164 TATTTTTAAAA-TTTAAAA
1 TATTTTTAAAATTTTAAAA
3959182 TCATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTTTTAAAATTTTAAAAAT
Found at i:3959178 original size:20 final size:21
Alignment explanation
Indices: 3959143--3959181 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3959133 ATTTAATTAA
*
3959143 TATTTTTACAATTTTAAAAAT
1 TATTTTTACAAATTTAAAAAT
3959164 TATTTTTA-AAATTTAAAA
1 TATTTTTACAAATTTAAAA
3959182 TCATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTTTTACAAATTTAAAAAT
Found at i:3964540 original size:9 final size:9
Alignment explanation
Indices: 3964513--3964543 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3964503 ATATGGTTGT
3964513 TTTTGGAAG
1 TTTTGGAAG
3964522 TTTATGGAAG
1 TTT-TGGAAG
3964532 TTTTGGAAG
1 TTTTGGAAG
3964541 TTT
1 TTT
3964544 GGTTGATAGA
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:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (9 bp):
TTTTGGAAG
Found at i:3966549 original size:12 final size:12
Alignment explanation
Indices: 3966532--3966574 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
3966522 TTCATACGTT
3966532 ATTATAATTGCA
1 ATTATAATTGCA
*
3966544 ATTATATAATCGCA
1 A-T-TATAATTGCA
3966558 ATTATAATTGCA
1 ATTATAATTGCA
3966570 ATTAT
1 ATTAT
3966575 TTCCCAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 15 0.56
13 2 0.07
14 10 0.37
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (12 bp):
ATTATAATTGCA
Found at i:3966553 original size:14 final size:14
Alignment explanation
Indices: 3966534--3966574 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
3966524 CATACGTTAT
3966534 TATAATTGCAATTA
1 TATAATTGCAATTA
*
3966548 TATAATCGCAA-T-
1 TATAATTGCAATTA
3966560 TATAATTGCAATTA
1 TATAATTGCAATTA
3966574 T
1 T
3966575 TTCCCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 11 0.48
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (14 bp):
TATAATTGCAATTA
Found at i:3967147 original size:27 final size:27
Alignment explanation
Indices: 3967109--3967165 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3967099 AAATACCTGA
*
3967109 CACCAGTGGAGGAACACGAAGTGGCGG
1 CACCAATGGAGGAACACGAAGTGGCGG
* * *
3967136 CACCAATGGAGGAATATGAAGTGGTGG
1 CACCAATGGAGGAACACGAAGTGGCGG
3967163 CAC
1 CAC
3967166 TAAGGGGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.37, T:0.12
Consensus pattern (27 bp):
CACCAATGGAGGAACACGAAGTGGCGG
Found at i:3967352 original size:12 final size:12
Alignment explanation
Indices: 3967335--3967371 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
3967325 CAAATAAGTG
3967335 GGAAAGAAAGAA
1 GGAAAGAAAGAA
3967347 GGAAAGAAAGAA
1 GGAAAGAAAGAA
*
3967359 GGAGAGGAAAGAA
1 GGA-AAGAAAGAA
3967372 AGAATAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
GGAAAGAAAGAA
Found at i:3970693 original size:21 final size:21
Alignment explanation
Indices: 3970667--3970713 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3970657 TTAGGGTCCA
*
3970667 ATTGCCCCGGAGGAGTAGAGT
1 ATTGCCCCGGAGGAGTAAAGT
*
3970688 ATTGCCCGGGAGGAGTAAAGT
1 ATTGCCCCGGAGGAGTAAAGT
3970709 ATTGC
1 ATTGC
3970714 GGTGGCTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (21 bp):
ATTGCCCCGGAGGAGTAAAGT
Found at i:3973168 original size:95 final size:94
Alignment explanation
Indices: 3972948--3973214 Score: 398
Period size: 93 Copynumber: 2.9 Consensus size: 94
3972938 TTATATTATT
*
3972948 TTTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAAT
1 TTTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAATAAAATAAAAT
***
3973013 TACTAACTA-ATTTTTTAAACATTATTAA
66 TACTAACTAGAAAATTTAAACATTATTAA
* * * *
3973041 ATTTTAAATCAATAAATATGAATAATGTTTTTTACTTACTACTACTACTAACAATAAAAGAAAAT
1 TTTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAATAAAATAAAAT
3973106 TACTAACTAGCAAAATTTAAACATTATTAA
66 TACTAACTAG-AAAATTTAAACATTATTAA
* *
3973136 TTTTTAAATCAATAAACATGAACAATATTTTTTAC-T--TGCTACTACTAACAATAAAATAAAAT
1 TTTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAATAAAATAAAAT
3973198 TACTAACTAGTAAAATT
66 TACTAACTAG-AAAATT
3973215 AAATTAAAAT
Statistics
Matches: 157, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
92 40 0.25
93 69 0.44
94 1 0.01
95 47 0.30
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.37
Consensus pattern (94 bp):
TTTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAATAAAATAAAAT
TACTAACTAGAAAATTTAAACATTATTAA
Found at i:3973203 original size:20 final size:21
Alignment explanation
Indices: 3973178--3973220 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3973168 TACTTGCTAC
3973178 TACTAAC-AATAAAATAAAAT
1 TACTAACTAATAAAATAAAAT
* *
3973198 TACTAACTAGTAAAATTAAAT
1 TACTAACTAATAAAATAAAAT
3973219 TA
1 TA
3973221 AAATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (21 bp):
TACTAACTAATAAAATAAAAT
Found at i:3973598 original size:13 final size:12
Alignment explanation
Indices: 3973580--3973633 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 12
3973570 CTTCTTCCCC
3973580 TTCTTCTCCTTTT
1 TTCTT-TCCTTTT
*
3973593 TTCTTCTTCTTTCT
1 TTCTT-TCCTTT-T
3973607 TTCTTTCTCTTTT
1 TTCTTTC-CTTTT
3973620 TTCTTT-CTTTT
1 TTCTTTCCTTTT
3973631 TTC
1 TTC
3973634 CCTCAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
11 8 0.22
13 19 0.51
14 10 0.27
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTTTCCTTTT
Found at i:3973617 original size:17 final size:18
Alignment explanation
Indices: 3973579--3973629 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
3973569 GCTTCTTCCC
*
3973579 CTTCTTC-TCCTTT-TTT
1 CTTCTTCTTTCTTTCTTT
3973595 CTTCTTCTTTCTTTCTTT
1 CTTCTTCTTTCTTTCTTT
*
3973613 C-TCTTTTTTCTTTCTTT
1 CTTCTTCTTTCTTTCTTT
3973630 TTTCCCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 7 0.23
17 20 0.65
18 4 0.13
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
CTTCTTCTTTCTTTCTTT
Found at i:3975114 original size:32 final size:31
Alignment explanation
Indices: 3975078--3975138 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
3975068 AACCCAATCC
* *
3975078 ATATTTTTTTAATTTTTAAAAATATTTATATT
1 ATATTATTTTAATATTTAAAAAT-TTTATATT
*
3975110 ATATTATTTTAATATTTAATAATTTTATA
1 ATATTATTTTAATATTTAAAAATTTTATA
3975139 CATTTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
ATATTATTTTAATATTTAAAAATTTTATATT
Found at i:3978019 original size:6 final size:6
Alignment explanation
Indices: 3978001--3978094 Score: 79
Period size: 6 Copynumber: 15.8 Consensus size: 6
3977991 TTAAATTGAT
* *
3978001 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TATCTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-T-TAAA
* ** *
3978048 TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA
3978095 CATTAAAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.06
5 8 0.11
6 48 0.67
7 7 0.10
8 5 0.07
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:3978051 original size:31 final size:30
Alignment explanation
Indices: 3977991--3978072 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 30
3977981 GACTTTTGAG
*
3977991 TTAAATTGATTTTAAATTT--AT-TTAAAT
1 TTAATTTGATTTTAAATTTAAATATTAAAT
3978018 TTAGATTT-ATTTTAAATTTAAATATCTAAAT
1 TTA-ATTTGATTTTAAATTTAAATAT-TAAAT
*
3978049 TTAATTTGAATTTAAATTTAAATA
1 TTAATTTGATTTTAAATTTAAATA
3978073 AAAATTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
27 14 0.30
28 3 0.06
29 2 0.04
30 5 0.11
31 23 0.49
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (30 bp):
TTAATTTGATTTTAAATTTAAATATTAAAT
Found at i:3978060 original size:25 final size:23
Alignment explanation
Indices: 3978010--3978094 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 23
3978000 TTTTAAATTT
* *
3978010 ATTTAAATTTAGATTTATTTTAA
1 ATTTAAATTTAAATTTAATTTAA
*
3978033 ATTTAAATATCTAAATTTAATTTGA
1 ATTTAAAT-T-TAAATTTAATTTAA
** *
3978058 ATTTAAATTTAAATAAAAATTAAA
1 ATTTAAATTTAAAT-TTAATTTAA
3978082 ATATTAAATTTAA
1 AT-TTAAATTTAA
3978095 CATTAAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 13 0.25
24 9 0.18
25 29 0.57
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAAATTTAAATTTAATTTAA
Found at i:3978066 original size:17 final size:16
Alignment explanation
Indices: 3978005--3978069 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
3977995 ATTGATTTTA
3978005 AATTT-ATTTAAATTT
1 AATTTAATTTAAATTT
*
3978020 AGATTTATTTTAAATTT
1 A-ATTTAATTTAAATTT
* *
3978037 AA-AT-ATCTAAATTT
1 AATTTAATTTAAATTT
3978051 AATTTGAATTTAAATTT
1 AATTT-AATTTAAATTT
3978068 AA
1 AA
3978070 ATAAAAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
14 10 0.26
15 3 0.08
16 5 0.13
17 21 0.54
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:3978068 original size:42 final size:42
Alignment explanation
Indices: 3978002--3978094 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
3977992 TAAATTGATT
* * ** *
3978002 TTAAATTT-ATTTAAATTTAGATTT-ATTTTAAATTTAAATA
1 TTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAATA
*
3978042 TCTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATA
1 T-TAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAATA
3978085 TTAAATTTAA
1 TTAAATTTAA
3978095 CATTAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
40 1 0.02
41 7 0.16
42 23 0.52
43 13 0.30
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (42 bp):
TTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAATA
Found at i:3978195 original size:13 final size:15
Alignment explanation
Indices: 3978178--3978214 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
3978168 ACCCATTTTT
3978178 TGGCCCAAATTA-AA
1 TGGCCCAAATTACAA
3978192 -GGCCC-AATTACAA
1 TGGCCCAAATTACAA
3978205 TGGCCCAAAT
1 TGGCCCAAAT
3978215 AGGCCCAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.25
13 7 0.35
14 5 0.25
15 3 0.15
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (15 bp):
TGGCCCAAATTACAA
Found at i:3979975 original size:30 final size:30
Alignment explanation
Indices: 3979933--3980165 Score: 340
Period size: 30 Copynumber: 7.8 Consensus size: 30
3979923 AAACAATTCG
* *
3979933 AAAATTACATTTTGACCCCAAAACTTTTCT
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* *
3979963 AAAATCATATTTTAACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* *
3979993 AAAATTATATTTTAACCCCAAAACTTTTCT
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* *
3980023 AAAATTATATTTTGACCCTAAAACTTTTAC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
3980053 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* *
3980083 AAAATTATATTTTAACCCTAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* *
3980113 AAAATCACATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* *
3980143 AAAATTACATTTTGACCCTAAAA
1 AAAATTATATTTTGACCCCAAAA
3980166 AATCTCATAA
Statistics
Matches: 183, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 183 1.00
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCAAAACTTTTCC
Found at i:3980219 original size:30 final size:30
Alignment explanation
Indices: 3980183--3980334 Score: 100
Period size: 30 Copynumber: 5.1 Consensus size: 30
3980173 TAAATCCCAT
*
3980183 TTTTAACCCCGATTTCACCAAAATTTACCA
1 TTTTAACCCCGATTTCACTAAAATTTACCA
* *
3980213 TTTTAACCCCGAAGCTT--CTAAAATTCTA--T
1 TTTTAACCCCG-A-TTTCACTAAAATT-TACCA
* * *
3980242 TTTTAACCTCGATTTTACTAAAAATTACCA
1 TTTTAACCCCGATTTCACTAAAATTTACCA
* *** ** *
3980272 TTTTACCCCCGAAACCTTTAGAA-TT-CCA
1 TTTTAACCCCGATTTCACTAAAATTTACCA
*
3980300 TTTTTAACCCCGATTTCACCAAAATTTACCA
1 -TTTTAACCCCGATTTCACTAAAATTTACCA
3980331 TTTT
1 TTTT
3980335 GCCCCCGGGT
Statistics
Matches: 88, Mismatches: 24, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
27 2 0.02
28 6 0.07
29 34 0.39
30 38 0.43
31 6 0.07
32 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTTAACCCCGATTTCACTAAAATTTACCA
Found at i:3980340 original size:59 final size:59
Alignment explanation
Indices: 3980174--3980341 Score: 230
Period size: 59 Copynumber: 2.8 Consensus size: 59
3980164 AAAATCTCAT
* * *
3980174 AAATCCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTAACCCCGAAGCTTCTA
1 AAATTCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGAACCTTCTA
* * * * *
3980233 AAATTCTATTTTTAACCTCGATTTTACTAAAAATTACCATTTTACCCCCGAAACCTT-TA
1 AAATTCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCG-AACCTTCTA
* *
3980292 GAATTCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTGCCCCCG
1 AAATTCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCG
3980342 GGTATCCATG
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
59 88 0.95
60 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (59 bp):
AAATTCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGAACCTTCTA
Found at i:3980360 original size:59 final size:59
Alignment explanation
Indices: 3980175--3980361 Score: 166
Period size: 59 Copynumber: 3.2 Consensus size: 59
3980165 AAATCTCATA
* * * *
3980175 AATCCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTAACCCCGAAGCT-TCTA-A
1 AATCCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCG--GGTATCCATG
* * * * * * * * *
3980234 AATTCTATTTTTAACCTCGATTTTACTAAAAATTACCATTTTACCCCC--GAAACCTTTAG
1 AATCCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGGGTATCC-AT-G
* *
3980293 AATTCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTGCCCCCGGGTATCCATG
1 AATCCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGGGTATCCATG
*
3980352 AGTCCCATTT
1 AATCCCATTT
3980362 CTTACCTTGA
Statistics
Matches: 98, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
56 1 0.01
59 92 0.94
60 1 0.01
61 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.35
Consensus pattern (59 bp):
AATCCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGGGTATCCATG
Found at i:3992275 original size:38 final size:38
Alignment explanation
Indices: 3992221--3992685 Score: 452
Period size: 38 Copynumber: 12.6 Consensus size: 38
3992211 GGTCTCAACG
* *
3992221 TCATCCCCTCGAAATTGAAGTGGAGTGGATAACACGTCT
1 TCAT-CCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
3992260 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACATCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
** *
3992298 TCATCTCC--GAAATTGAAGTA-A---GAGCA-ACGTCA
1 TCATC-CCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
3992330 TC--CCCTTGAAATTAAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
3992366 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
** *
3992404 TCATCTCC--GAAATTGAAGTA-A---GAGCA-ACGTCA
1 TCATC-CCTTGAAATTGAAGTAGAGTGGATAACACGTCT
3992436 TC--CCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* **
3992472 TCATCCCTTGAAATTGAAGTAGAGTGGATAACAGAGTGGA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACA-CGT-CT
* * ** * * * * * *
3992512 TAATACGTCTTGATCTCTGAAATTGAAGT-AAGAGCAACGTCA
1 TCAT-C-CCTTGAAAT-TGAAGTAG-AGTGGATAAC-ACGTCT
*
3992554 TC--CCCTTGAAATTAAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
3992590 TCATCCCTTGAAATTGAAGTAGAGTGGATAACGCGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
3992628 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
3992666 TCATCTC-TGAAATTGAAGTA
1 TCATCCCTTGAAATTGAAGTA
3992686 AGAGCAACGT
Statistics
Matches: 349, Mismatches: 47, Indels: 62
0.76 0.10 0.14
Matches are distributed among these distances:
29 4 0.01
30 2 0.01
31 23 0.07
32 15 0.04
33 6 0.02
35 6 0.02
36 26 0.07
37 45 0.13
38 184 0.53
39 11 0.03
40 3 0.01
41 1 0.00
42 8 0.02
43 11 0.03
44 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (38 bp):
TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
Done.