Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007867.1 Hibiscus syriacus cultivar Beakdansim tig00110239_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3477501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:209732 original size:20 final size:20
Alignment explanation
Indices: 209709--209762 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
209699 TTGACTTCTG
209709 TGTTGCGAATTACAAATTCA
1 TGTTGCGAATTACAAATTCA
209729 TGTTGCGAATTACAAATTCA
1 TGTTGCGAATTACAAATTCA
*
209749 TGTTGCGATTTACA
1 TGTTGCGAATTACA
209763 TTATCGAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTTGCGAATTACAAATTCA
Found at i:210652 original size:15 final size:15
Alignment explanation
Indices: 210632--210666 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
210622 GGATAACTTG
210632 TTTTATT-TTAATAAT
1 TTTTATTCTTAAT-AT
210647 TTTTATTCTTAATAT
1 TTTTATTCTTAATAT
210662 TTTTA
1 TTTTA
210667 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATTCTTAATAT
Found at i:211079 original size:30 final size:31
Alignment explanation
Indices: 211044--211111 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
211034 CAAAAAGTTG
*
211044 CAAAATGA-TATT-TACTTTAAT-AAATTATTA
1 CAAAATGATTATTATA-TTT-ATCAAACTATTA
*
211074 CAAAATAATTATTATATTTATCAAACTATTA
1 CAAAATGATTATTATATTTATCAAACTATTA
211105 CAAAATG
1 CAAAATG
211112 GGTCTCAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 9 0.28
31 21 0.66
32 2 0.06
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (31 bp):
CAAAATGATTATTATATTTATCAAACTATTA
Found at i:214597 original size:55 final size:53
Alignment explanation
Indices: 214539--214976 Score: 461
Period size: 55 Copynumber: 8.0 Consensus size: 53
214529 GGATAAATGA
* * * *
214539 AACTTGAAAAATCTTCAAATGACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAA
1 AACTCGAACAATCTTCAAA--ACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
* * * *
214594 AACTCGAACAATCTTCAGTAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-
1 AACTCGAACAATCTTCA--AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
* * *
214648 AGACTCGAACAATCTTCAGAAACAGGTCCGCTCTCTATTCCTTCAGAGAGGATAG
1 A-ACTCGAACAATCTTCA-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
* *
214703 AACTCGAACAATCTTCAACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAG
1 AACTCGAACAATCTTC-A-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
* ** * *
214758 AACTCGAACAATCTTTAACAAATAGGTCCGCTCCCTATTCATTCAGGGAGTATAG
1 AACTCGAACAATC-TTCA-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
* * *
214813 AACTCGAACAATCTTAACAAATGGGTCCTCTCCCTATT-CTATCAGAGAGTATAG
1 AACTCGAACAATCTTCA-AAACGGGTCCGCTCCCTATTCCT-TCAGAGAGTATAG
* *
214867 AACTCGAACAATCTTCAAAAAACGGGTTCGCTCCTTATT-CTATCAGAGAGTATAG
1 AACTCGAACAATCTTC--AAAACGGGTCCGCTCCCTATTCCT-TCAGAGAGTATAG
* *
214922 AACTCGAACAATCTTTAACAAACGGGTTCGCTCCCTATT-CTATCAGAGAGTATAG
1 AACTCGAACAATC-TTCA-AAACGGGTCCGCTCCCTATTCCT-TCAGAGAGTATAG
214977 GACTTGATCT
Statistics
Matches: 337, Mismatches: 35, Indels: 22
0.86 0.09 0.06
Matches are distributed among these distances:
53 1 0.00
54 95 0.28
55 234 0.69
56 5 0.01
57 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (53 bp):
AACTCGAACAATCTTCAAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
Found at i:214710 original size:109 final size:109
Alignment explanation
Indices: 214539--214976 Score: 539
Period size: 109 Copynumber: 4.0 Consensus size: 109
214529 GGATAAATGA
* * * * * *
214539 AACTTGAAAAATCTTCAAATGACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAAACTCGAACA
1 AACTCGAACAATCTTCAAA-AACAGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACA
** * *
214604 ATCTTCAGTAAACGTGTCTGCTCCCTATTCGT-TCAGGGAGTATA-
65 ATCTTCAACAAACGGGTCTGCTCCCTATTC-TATCAGAGAGTATAG
* * *
214648 AGACTCGAACAATCTTCAGAAACAGGTCCGCTCTCTATTCCTTCAGAGAGGATAGAACTCGAACA
1 A-ACTCGAACAATCTTCAAAAACAGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACA
*
214713 ATCTTCAACAAACGGGTCTGCTCTCTATTCCT-TCAGAGAGTATAG
65 ATCTTCAACAAACGGGTCTGCTCCCTATT-CTATCAGAGAGTATAG
* * * *
214758 AACTCGAACAATCTTTAACAAATAGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACA
1 AACTCGAACAATCTTCAA-AAACAGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACA
*
214823 ATCTT-AACAAATGGGTCCT-CTCCCTATTCTATCAGAGAGTATAG
65 ATCTTCAACAAACGGGT-CTGCTCCCTATTCTATCAGAGAGTATAG
* * *
214867 AACTCGAACAATCTTCAAAAAACGGGTTCGCTCCTTATT-CTATCAGAGAGTATAGAACTCGAAC
1 AACTCGAACAATCTTC-AAAAACAGGTCCGCTCCCTATTCCT-TCAGAGAGTATAGAACTCGAAC
*
214931 AATCTTTAACAAACGGGT-TCGCTCCCTATTCTATCAGAGAGTATAG
64 AATCTTCAACAAACGGGTCT-GCTCCCTATTCTATCAGAGAGTATAG
214977 GACTTGATCT
Statistics
Matches: 287, Mismatches: 31, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
108 4 0.01
109 181 0.63
110 102 0.36
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (109 bp):
AACTCGAACAATCTTCAAAAACAGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAA
TCTTCAACAAACGGGTCTGCTCCCTATTCTATCAGAGAGTATAG
Found at i:214820 original size:164 final size:162
Alignment explanation
Indices: 214539--214980 Score: 527
Period size: 164 Copynumber: 2.7 Consensus size: 162
214529 GGATAAATGA
* * ** * * *
214539 AACTTGAAAAATCTTCAAATGACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAAACTCGAACA
1 AACTCGAACAATCTTCAAAAAACGGGTCTGCT-CCTATTCCTTCAGAGAGTATAGAACTCGAACA
* ** * * * *
214604 ATCTTCAGTAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCAGA
65 ATCTTTAACAAAAG-GTCCGCTCCCTATTC-TTCAGGGAGTATAGAGACTCGAACAATCTTAACA
*
214668 AACAGGTCCGCTCTCTATTCCT-TCAGAGAGGATAG
128 AACAGGTCCGCTCCCTATT-CTATCAGAGAGGATAG
*
214703 AACTCGAACAATCTTCAACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACA
1 AACTCGAACAATCTTCAAAAAACGGGTCTGCTC-CTATTCCTTCAGAGAGTATAGAACTCGAACA
214768 ATCTTTAACAAATAGGTCCGCTCCCTATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTAACA
65 ATCTTTAACAAA-AGGTCCGCTCCCTATTC-TTCAGGGAGTATAGAGACTCGAACAATCTTAACA
** * *
214832 AATGGGTCCTCTCCCTATTCTATCAGAGAGTATAG
128 AACAGGTCCGCTCCCTATTCTATCAGAGAGGATAG
214867 AACTCGAACAATCTTCAAAAAACGGGT-TCGCTCCTTATT-CTATCAGAGAGTATAGAACTCGAA
1 AACTCGAACAATCTTCAAAAAACGGGTCT-GCTCC-TATTCCT-TCAGAGAGTATAGAACTCGAA
* * *
214930 CAATCTTTAACAAACGGGTTCGCTCCCTATTCTATCAGAGAGTATAG-GACT
63 CAATCTTTAACAAA-AGGTCCGCTCCCTATTCT-TCAGGGAGTATAGAGACT
214981 TGATCTTCAT
Statistics
Matches: 243, Mismatches: 26, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
163 8 0.03
164 233 0.96
165 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (162 bp):
AACTCGAACAATCTTCAAAAAACGGGTCTGCTCCTATTCCTTCAGAGAGTATAGAACTCGAACAA
TCTTTAACAAAAGGTCCGCTCCCTATTCTTCAGGGAGTATAGAGACTCGAACAATCTTAACAAAC
AGGTCCGCTCCCTATTCTATCAGAGAGGATAG
Found at i:215049 original size:37 final size:38
Alignment explanation
Indices: 214994--215065 Score: 137
Period size: 37 Copynumber: 1.9 Consensus size: 38
214984 TCTTCATAAA
214994 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAT
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAT
215032 ATGA-TTTGCTTCACTACTCTTCCGTGAAGGCTTA
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTA
215066 AGATTAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 30 0.88
38 4 0.12
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (38 bp):
ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAT
Found at i:216388 original size:24 final size:23
Alignment explanation
Indices: 216356--216402 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
216346 CTTTTATTTC
216356 TTTTTCTTTATC-TTTTTAATCAT
1 TTTTTCTTT-TCATTTTTAATCAT
*
216379 TTTTTCCTTTTCATTTTTCATCAT
1 TTTTT-CTTTTCATTTTTAATCAT
216403 ATTTCATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTCTTTTCATTTTTAATCAT
Found at i:216439 original size:8 final size:8
Alignment explanation
Indices: 216421--216485 Score: 55
Period size: 8 Copynumber: 8.5 Consensus size: 8
216411 TTTTTCTCAC
216421 TTTTC-TT
1 TTTTCTTT
216428 TTTTCTTT
1 TTTTCTTT
*
216436 TTTT-TTC
1 TTTTCTTT
*
216443 TTTTCATT
1 TTTTCTTT
*
216451 TTTTC-AT
1 TTTTCTTT
*
216458 TTTTCATT
1 TTTTCTTT
*
216466 TTTCCTTT
1 TTTTCTTT
*
216474 TCTTCTTT
1 TTTTCTTT
216482 TTTT
1 TTTT
216486 TTATTTATTT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
7 17 0.38
8 28 0.62
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTCTTT
Found at i:216496 original size:36 final size:37
Alignment explanation
Indices: 216411--216514 Score: 95
Period size: 36 Copynumber: 2.8 Consensus size: 37
216401 ATATTTCATT
* * * *
216411 TTTTTCTCACTTTTCTTTTTTCTTTTTTTTTCTTTTCA
1 TTTTT-TCATTTTTCATTTTTCTCTTTTCTTCTTTTCA
*
216449 TTTTTTCATTTTTCATTTTTC-CTTTTCTTCTTTT-T
1 TTTTTTCATTTTTCATTTTTCTCTTTTCTTCTTTTCA
* * * *
216484 TTTTATTTATTTTTTATTTTTTTCATTTCTT
1 TTTT-TTCATTTTTCATTTTTCTCTTTTCTT
216515 TTTCAGGAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
35 4 0.07
36 25 0.45
37 21 0.38
38 5 0.09
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (37 bp):
TTTTTTCATTTTTCATTTTTCTCTTTTCTTCTTTTCA
Found at i:216501 original size:7 final size:7
Alignment explanation
Indices: 216421--216505 Score: 55
Period size: 7 Copynumber: 11.6 Consensus size: 7
216411 TTTTTCTCAC
*
216421 TTTTCTT
1 TTTTATT
*
216428 TTTTCTT
1 TTTTATT
*
216435 TTTTTTT
1 TTTTATT
216442 CTTTTCATT
1 -TTTT-ATT
216451 TTTTCATT
1 TTTT-ATT
*
216459 TTTCATT
1 TTTTATT
**
216466 TTTCCTT
1 TTTTATT
*
216473 TTCTTCTT
1 TT-TTATT
216481 TTTT-TT
1 TTTTATT
216487 TATTTATT
1 T-TTTATT
216495 TTTTATT
1 TTTTATT
216502 TTTT
1 TTTT
216506 TCATTTCTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
6 3 0.04
7 39 0.57
8 24 0.35
9 2 0.03
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTATT
Found at i:216505 original size:20 final size:20
Alignment explanation
Indices: 216480--216517 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
216470 CTTTTCTTCT
*
216480 TTTTTTTTATTTATTTTTTA
1 TTTTTTTCATTTATTTTTTA
*
216500 TTTTTTTCATTTCTTTTT
1 TTTTTTTCATTTATTTTT
216518 CAGGAGAAAT
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:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTTCATTTATTTTTTA
Found at i:216506 original size:45 final size:46
Alignment explanation
Indices: 216404--216511 Score: 127
Period size: 45 Copynumber: 2.4 Consensus size: 46
216394 TTTCATCATA
* *
216404 TTTCATTTTTTTCTCACTTTTCTTTTTTCTTTTTTTTTCTTTTCATTT
1 TTTCA-TTTTTT-TCATTTTTCTTTTTTCTTTTTTTTTCATTTCATTT
216452 TTTCA--TTTTTCATTTTTCCTTTTCTTCTTTTTTTTT-ATTT-ATTT
1 TTTCATTTTTTTCATTTTT-CTTTT-TTCTTTTTTTTTCATTTCATTT
216496 TTT-ATTTTTTTCATTT
1 TTTCATTTTTTTCATTT
216512 CTTTTTCAGG
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
43 1 0.02
44 14 0.26
45 22 0.41
46 12 0.22
48 5 0.09
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (46 bp):
TTTCATTTTTTTCATTTTTCTTTTTTCTTTTTTTTTCATTTCATTT
Found at i:216518 original size:43 final size:42
Alignment explanation
Indices: 216412--216518 Score: 103
Period size: 44 Copynumber: 2.4 Consensus size: 42
216402 TATTTCATTT
216412 TTTTCTCACTTTTCTTTTTTCTTTTTTTTTCTTTTCATTTTTTCA
1 TTTT-TCA-TTTTC-TTTTTCTTTTTTTTTCTTTTCATTTTTTCA
* *
216457 TTTTTCATTTTTCCTTTTCTTCTTTTTTT-TTATTTATTTTTT-A
1 TTTTTCA-TTTTCTTTTTCTT-TTTTTTTCTT-TTCATTTTTTCA
216500 TTTTTTTCA-TTTCTTTTTC
1 --TTTTTCATTTTCTTTTTC
216519 AGGAGAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
43 19 0.35
44 24 0.44
45 11 0.20
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (42 bp):
TTTTTCATTTTCTTTTTCTTTTTTTTTCTTTTCATTTTTTCA
Found at i:220307 original size:17 final size:17
Alignment explanation
Indices: 220275--220308 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
220265 CAGCCAATCT
*
220275 GACCTTTCTCATTTCCC
1 GACCTTTCTCAATTCCC
*
220292 GACCTTTCTTAATTCCC
1 GACCTTTCTCAATTCCC
220309 CTTAGCTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.38, G:0.06, T:0.41
Consensus pattern (17 bp):
GACCTTTCTCAATTCCC
Found at i:222888 original size:228 final size:227
Alignment explanation
Indices: 222466--222920 Score: 865
Period size: 228 Copynumber: 2.0 Consensus size: 227
222456 CCCTTAAGGT
*
222466 TGACAAAAAGCATATTTGTTTCTCCTCTTCCAATGGTGGATAGACTTGCACCACTACATCTCTCT
1 TGACAAAAAGCATATTTGTTTCTCCTCTTCCAATGGTGGATAGACTTGCACCACTACATCTCTCC
*
222531 ATCTTTGAGCATATTGTCTAAAACTCTCGTTAGACTTCTTTTCCATTCATTGCAGCATCATCCTG
66 ATCTTTGAGCATATTGTCTAAAACTCTCGTTAGACTTCTTTTCCATTCATTGCAACATCATCCTG
222596 TTGGGCCTAACATCTTTTACATGTTTGTATTGCTCAAGAAAGAACTTAGCCAAGTCTTTCCACGA
131 TTGGGCCTAACATCTTTTACATGTTTGTATTGCTCAAGAAAGAACTTAGCCAAGTCTTTCCACGA
*
222661 TTTAATATTAGCTCTACTCAGCTGGTTATACC
196 TTTAATATTAGCTATACTCAGCTGGTTATACC
*
222693 TGACAAAAAGCATATTTGTTTCCTCTTCTTCCAATGGTGGATAGACTTGCACCACTACATCTCTC
1 TGACAAAAAGCATATTTGTTT-CTCCTCTTCCAATGGTGGATAGACTTGCACCACTACATCTCTC
222758 CATCTTTGAGCATATTGTCTAAAACTCTCGTTAGACTTCTTTTCCATTCATTGCAACATCATCCT
65 CATCTTTGAGCATATTGTCTAAAACTCTCGTTAGACTTCTTTTCCATTCATTGCAACATCATCCT
222823 GTTGGGCCTAACATCTTTTACATGTTTGTATTGCTCAAGAAAGAACTTAGCCAAGTCTTTCCACG
130 GTTGGGCCTAACATCTTTTACATGTTTGTATTGCTCAAGAAAGAACTTAGCCAAGTCTTTCCACG
222888 ATTTAATATTAGCTATACTCAGCTGGTTATACC
195 ATTTAATATTAGCTATACTCAGCTGGTTATACC
222921 ACCGGATTGC
Statistics
Matches: 223, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
227 21 0.09
228 202 0.91
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (227 bp):
TGACAAAAAGCATATTTGTTTCTCCTCTTCCAATGGTGGATAGACTTGCACCACTACATCTCTCC
ATCTTTGAGCATATTGTCTAAAACTCTCGTTAGACTTCTTTTCCATTCATTGCAACATCATCCTG
TTGGGCCTAACATCTTTTACATGTTTGTATTGCTCAAGAAAGAACTTAGCCAAGTCTTTCCACGA
TTTAATATTAGCTATACTCAGCTGGTTATACC
Found at i:229340 original size:3 final size:3
Alignment explanation
Indices: 229332--229370 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
229322 CCATTTTTAA
* *
229332 TAT TAT TAT TAT TAT TAT TAT TAAT TAT AAT TAT CAT TA
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TA
229371 CATTTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:235807 original size:5 final size:5
Alignment explanation
Indices: 235799--235830 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
235789 TGATTGTTAA
235799 TATTT TATTT TATTT TATTT TATTT TAATTT T
1 TATTT TATTT TATTT TATTT TATTT T-ATTT T
235831 TGCAGGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:236552 original size:131 final size:132
Alignment explanation
Indices: 236311--236653 Score: 406
Period size: 131 Copynumber: 2.6 Consensus size: 132
236301 GTAATAACTT
** * * * *
236311 TTCATTTCGGTTGGAGTTATAAATGACTGCTTTAAGGCATGAGAGGTCATTCATTCTCGATCGAA
1 TTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
* ** * * *
236376 AATAATTTGATATTA-CAAATTTCTTTTGAATCAATATTGATTTTTAAGACGGAATAGTGATATC
66 AATAATTAGATATTATCAAATTTCACTCGAATCAATATTGATTTTTAAGACGAAATAGTGATATA
236440 TC
131 TC
* * *
236442 TTCATTTCAATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTTGATTGGA
1 TTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
* ** *
236507 AATCATTAGATATTATC-GTTTTCACTCGAATCGATATTAGA-TTTTAAGACGAAATAGTGATAT
66 AATAATTAGATATTATCAAATTTCACTCGAATCAATATT-GATTTTTAAGACGAAATAGTGATAT
236570 ATC
130 ATC
* * * * * * *
236573 TTCATTTCAATTGGGGTAATAAAGGAATG-TGTTAAGGCATGAAAGATTATTTATTCTCGATTAG
1 TTCATTTCAATTGGAGTAATAAATGACTGCT-TTAAGGCATGAGAGGTCATTTATTCTCGATTGG
236637 AAATAATTAGATATTAT
65 AAATAATTAGATATTAT
236654 AATACTTTCT
Statistics
Matches: 179, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
130 1 0.01
131 175 0.98
132 3 0.02
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (132 bp):
TTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
AATAATTAGATATTATCAAATTTCACTCGAATCAATATTGATTTTTAAGACGAAATAGTGATATA
TC
Found at i:238850 original size:19 final size:19
Alignment explanation
Indices: 238828--238864 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
238818 CATCAGAGTA
238828 AAAGGTTTTCATGATGGAC
1 AAAGGTTTTCATGATGGAC
238847 AAAGGTTTTCATGATGGA
1 AAAGGTTTTCATGATGGA
238865 GTAAACTATA
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:0.32, C:0.08, G:0.27, T:0.32
Consensus pattern (19 bp):
AAAGGTTTTCATGATGGAC
Found at i:244072 original size:41 final size:43
Alignment explanation
Indices: 244022--244115 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 43
244012 CCAAAATAGG
* *
244022 TAAAGTCCTTCGGGCCATCAGTAA-TCTTTCGAGCATGATGCT
1 TAAAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCAAGATGCT
* * * *
244064 TAAA-TCCTTTGGGACATCTGTAAGTTTTTCGAGCAAGATG-A
1 TAAAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCAAGATGCT
244105 T-AAGTCCTTCG
1 TAAAGTCCTTCG
244116 AACCATCCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
40 2 0.05
41 23 0.53
42 18 0.42
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (43 bp):
TAAAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCAAGATGCT
Found at i:245055 original size:41 final size:42
Alignment explanation
Indices: 244958--245058 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
244948 CCAAAATTGG
* * * * *
244958 TAAGTCATTTGGGCCATCAGTGAGTCTTTCAAGCATGATGCT
1 TAAGTCATTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGCA
* * * *
245000 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG-A
1 TAAGTCATTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGCA
245041 TAAGTCATTCGGGTCATC
1 TAAGTCATTCGGGTCATC
245059 CAAAAAACCT
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 16 0.33
42 32 0.67
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (42 bp):
TAAGTCATTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGCA
Found at i:245184 original size:233 final size:233
Alignment explanation
Indices: 243984--245610 Score: 2060
Period size: 235 Copynumber: 7.0 Consensus size: 233
243974 CATTTCCTTC
* * *
243984 GAAAAGTTTTTTACCTAGTAAACTATTCCCAAAATAGGTAAAGTCCTTCGGGCCATCAGTAA-TC
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGT-AAGTCCTTCGGGCCATCAGTAAGTC
* * *
244048 TTTCGAGCATGATGCTTAAATCCTTTGGGACATCTGTAAGTTTTTCGAGCAAGATGATAAGTCCT
65 TTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCT
**
244113 TCGAACCATCCACAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAAAAAATGAGAAAAGT
130 TCGGGCCATCCACAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTC-AAAAAATGAGAAAAGT
* * *
244178 TTCTCATTTAAATATAAAAATTGAAATATTTGAAAAGTAA
194 TTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
* ** * * *
244218 GAAAAATTTCTTACCTAGTAAACTATTTCTGAAATGGGTAAAGTCATTTGGGCCATCAGTAAGTC
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGT-AAGTCCTTCGGGCCATCAGTAAGTC
* * * *
244283 TTTTGAGCATGATGCTTAAATCCTTCGGGTTATCTGTAAGTCTTTCGAGTAAGATGATAAGTCAT
65 TTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCT
* *
244348 TCGGGCCATCCACAAGACCTTTGGGCAGGATGTTTTCACAT-TATTTTCAAAAAAATGAGAAAAG
130 TCGGGCCATCCACAAGACCTTTGGGCAGGATGTTTTCACATGT-CTCTC-AAAAAATGAGAAAAG
* * * *
244412 TTTCTCATTTATATCTAAAAATTTAAATTTTTTTAAAAGTAA
193 TTTCTCATTTAAATCTGAAAATTGAAA-TTTTTGAAAAGTAA
*
244454 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTGAGTCT
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCT
* * ** * * *
244519 TTCAAGCATAATGCTTAAATCCTTCGGGTCATCTGTAAGTAATTCGAGAAATATAATAAGTCCTT
66 TTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTT
* * * * *
244584 CGGGCCATCCAGAAGACCTTCGGGCAGGAAG-TTTCACATGTCTCTCAAAAAATAAAAAACAAAG
131 CGGGCCATCCACAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAAAAAT--GAGA-AAAG
* * *
244648 TTTCTCATTTAAATATGAAAATTGAAAATTTTGAAAAGCAA
193 TTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
* ** *
244689 GAAAAATTTCTTACCTAGTAAACTATTTCCAAAA-TAATAAGTCCTTTGGGCCATCAGTAAGTCT
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCT
* * * *
244753 TTCGAGCATGATGCTTAAATCCTTCAGGTTATATGTAAGTCTTT-GAGCAAGATGATAAGTCATT
66 TTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTT
* * *
244817 TGGGCCATCCACAAGACCTTTGGACAGGATGGTTTCACATGT-TCTTCGAAAAAATGAGAAATA-
131 CGGGCCATCCACAAGACCTTTGGGCAGGATGTTTTCACATGTCTC-TC-AAAAAATGAGAAA-AG
* *
244880 TTTCTCATTTAAATCT-AAAATTGAAATTTGTGAAAAGTAT
193 TTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
* * *
244920 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTTGGGCCATCAGTGAGTCT
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCT
* *
244985 TTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATT
66 TTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTT
* * * * *
245050 CGGGTCATCCAAAAAACCTTCGGGTAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAAGTTT
131 CGGGCCATCCACAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAAGTTT
* **
245115 CCCATTTAAATCTGAAAATTGATCTTTTTGAAAAGTAA
196 CTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
* *
245153 GAAAAGTTTCTTACCTTGTAAACTATTTCCAAAATT-GTAAGTCCTTCGTGCCATCAGTAAGTCT
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCT
*
245217 TTTGAGCATGATGCTTAAA---------TC--C--TAAGTCTTTCGAGCAAGATGATAAGTCCTT
66 TTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTT
* * *
245269 CGGGCCATCCACGAA-ACCTTTGGGCAGGATGTTTTCACATGTTTTTCAAAAAATGATAAAAGTT
131 CGGGCCATCCAC-AAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAAGTT
245333 TCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
195 TCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
* * * *
245372 GAAAAATTTCTTACCTAGTAAACTATTTCAAAAATTAGTAAGTCCTTCGGGCCATCAGTGAGTCT
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCT
* * * *
245437 TTTGAGCATGATG-TGTAAATCCTTCGAGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCT
66 TTCGAGCATGATGCT-TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCT
* * * ** * * * ** *
245501 TCAGGCTATCCATAAGACCTTCAGGCATGATGTTTTCACATGTTTTTTTGAAGAATGAGAAAAGT
130 TCGGGCCATCCACAAGACCTTTGGGCAGGATGTTTTCACATG-TCTCTCAAAAAATGAGAAAAGT
* * * *
245566 TTCTCATTTATATTTGAAAATTGAAATATTTAAAAAGTAA
194 TTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
*
245606 AAAAA
1 GAAAA
245611 AACAATTTCC
Statistics
Matches: 1215, Mismatches: 144, Indels: 68
0.85 0.10 0.05
Matches are distributed among these distances:
219 153 0.13
220 45 0.04
221 1 0.00
223 2 0.00
229 2 0.00
231 55 0.05
232 154 0.13
233 226 0.19
234 201 0.17
235 302 0.25
236 74 0.06
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (233 bp):
GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCT
TTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTT
CGGGCCATCCACAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAAGTTT
CTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
Found at i:245431 original size:452 final size:454
Alignment explanation
Indices: 243984--245611 Score: 2090
Period size: 452 Copynumber: 3.5 Consensus size: 454
243974 CATTTCCTTC
* * *
243984 GAAAAGTTTTTTACCTAGTAAACTATTCCCAAAA-TAGGTAAAGTCCTTCGGGCCATCAGT-AAT
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTA-GT-AAGTCCTTCGGGCCATCAGTGAGT
* * * *
244047 CTTTCGAGCATGATGCTTAAATCCTTTGGGACATCTGTAAGTTTTTCGAGCAAGATGATAAGTCC
64 CTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCC
** * *
244112 TTCGAACCATCCACAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAAAAAATGAGAAAAG
129 TTCGGGCCATCCAAAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTC-AAAAAATGAGAAAAG
* *
244177 TTTCTCATTTAAATATAAAAATTGAAATATTTGAAAAGTAAGAAAAATTTCTTACCTAGTAAACT
193 TTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAATTTCTTACCTAGTAAACT
** * *
244242 ATTTCTGAAATGGGTAAAGTCATTTGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCT
258 ATTTCCAAAAT-AGT-AAGTCCTTTGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAA----
*
244307 TCGGGTTATCTGTAAGTCTTTCGAGTAAGATGATAAGTCATTCGGGCCATCCACAAGACCTTTGG
317 TC------TCT-TAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCACAAGACCTTTGG
* *
244372 GCAGGATGTTTTCACAT-TATTTTCAAAAAAATGAGAAAAGTTTCTCATTTATATCTAAAAATTT
375 GCAGGATGTTTTCACATGT-TTTTCAAAAAAATGAGAAAAGTTTCTCATTTAAATCT-AAAATTG
*
244436 AAATTTTTTTAAAAGTAA
438 AAA-TTTTTGAAAAGTAA
*
244454 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTGAGTCT
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAGTAAGTCCTTCGGGCCATCAGTGAGTCT
* ** * * *
244519 TTCAAGCATAATGCTTAAATCCTTCGGGTCATCTGTAAGTAATTCGAGAAATATAATAAGTCCTT
66 TTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTT
* * * *
244584 CGGGCCATCCAGAAGACCTTCGGGCAGGAAG-TTTCACATGTCTCTCAAAAAATAAAAAACAAAG
131 CGGGCCATCCAAAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAAT--GAGA-AAAG
* *
244648 TTTCTCATTTAAATATGAAAATTGAAAATTTTGAAAAGCAAGAAAAATTTCTTACCTAGTAAACT
193 TTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAATTTCTTACCTAGTAAACT
* *
244713 ATTTCCAAAATAATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTC
258 ATTTCCAAAATAGTAAGTCCTTTGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAAT-C-TC
* *
244778 AGGTTATATGTAAGTCTTT-GAGCAAGATGATAAGTCATTTGGGCCATCCACAAGACCTTTGGAC
321 --------T-TAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCACAAGACCTTTGGGC
* * *
244842 AGGATGGTTTCACATGTTCTTCGAAAAAATGAGAAATA-TTTCTCATTTAAATCTAAAATTGAAA
377 AGGATGTTTTCACATGTTTTTCAAAAAAATGAGAAA-AGTTTCTCATTTAAATCTAAAATTGAAA
* *
244906 TTTGTGAAAAGTAT
441 TTTTTGAAAAGTAA
* * *
244920 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTTGGGCCATCAGTGAGTCT
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAGTAAGTCCTTCGGGCCATCAGTGAGTCT
*
244985 TTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATT
66 TTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTT
* * *
245050 CGGGTCATCCAAAAAACCTTCGGGTAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAAGTTT
131 CGGGCCATCCAAAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAAGTTT
* * ** * *
245115 CCCATTTAAATCTGAAAATTGATCTTTTTGAAAAGTAAGAAAAGTTTCTTACCTTGTAAACTATT
196 CTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATT
* * *
245180 TCCAAAATTGTAAGTCCTTCGTGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATC-C-TAAG
261 TCCAAAATAGTAAGTCCTTTGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCTCTTAAG
*
245243 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCACGAA-ACCTTTGGGCAGGATGTTTTCAC
326 TCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCAC-AAGACCTTTGGGCAGGATGTTTTCAC
*
245307 ATGTTTTTC-AAAAAATGATAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTA
390 ATGTTTTTCAAAAAAATGAGAAAAGTTTCTCATTTAAATCT-AAAATTGAAATTTTTGAAAAGTA
245371 A
454 A
* *
245372 GAAAAATTTCTTACCTAGTAAACTATTTCAAAAATTAGTAAGTCCTTCGGGCCATCAGTGAGTCT
1 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAGTAAGTCCTTCGGGCCATCAGTGAGTCT
** * * *
245437 TTTGAGCATGATG-TGTAAATCCTTCGAGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCT
66 TTCAAGCATGATGCT-TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCT
* * * * * * * ** *
245501 TCAGGCTATCCATAAGACCTTCAGGCATGATGTTTTCACATGTTTTTTTGAAGAATGAGAAAAGT
130 TCGGGCCATCCAAAAGACCTTCGGGCAGGATGTTTTCACATG-TCTCTCAAAAAATGAGAAAAGT
* * * * *
245566 TTCTCATTTATATTTGAAAATTGAAATATTTAAAAAGTAAAAAAAA
194 TTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAA
245612 ACAATTTCCA
Statistics
Matches: 1023, Mismatches: 112, Indels: 63
0.85 0.09 0.05
Matches are distributed among these distances:
450 1 0.00
451 38 0.04
452 231 0.23
453 56 0.05
461 3 0.00
463 1 0.00
464 116 0.11
465 3 0.00
466 159 0.16
467 31 0.03
468 95 0.09
469 91 0.09
470 123 0.12
471 75 0.07
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (454 bp):
GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAGTAAGTCCTTCGGGCCATCAGTGAGTCT
TTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTT
CGGGCCATCCAAAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAAGTTT
CTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATT
TCCAAAATAGTAAGTCCTTTGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCTCTTAAG
TCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCACAAGACCTTTGGGCAGGATGTTTTCACA
TGTTTTTCAAAAAAATGAGAAAAGTTTCTCATTTAAATCTAAAATTGAAATTTTTGAAAAGTAA
Found at i:246258 original size:134 final size:134
Alignment explanation
Indices: 245906--246595 Score: 757
Period size: 134 Copynumber: 5.2 Consensus size: 134
245896 ATCGAACTCA
* ** * * * * *
245906 ATTCAATCTTTCCTGAAGAGTAGTAGAATAAATCAACATTCCCAGATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATATGATTTTTCCTCAAGAA
* * * * * * *
245971 GAAGCAGAATATATCACTCTCTTTCAAGATTTGATATTCCTTGAGGAATATTGGAACAAATC-AG
66 GAAGCAGAATAAATCCCTCTCTTTCAAGATTTGATCTTCCTTGAGTAACAGTGGAACAAGTCTA-
246035 CCTCG
130 CCTCG
* * *
246040 ATTCAATCTT-CCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATATGGTTTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATATGATTTTTCCTCAAGAA
** * * * *
246104 GAAGTGGAACAAATCCCTTTCTTTCAAGATTTGATCTTCCTTAAGTAACAGTGGAACAAGTCTAA
66 GAAGCAGAATAAATCCCTCTCTTTCAAGATTTGATCTTCCTTGAGTAACAGTGGAACAAGTCTAC
246169 CTCG
131 CTCG
* * * *
246173 ATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATCCCCAGATTTTATTTTTGCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATATGATTTTTCCTCAAGAA
* ** * ** ** *
246238 GAAGC---A-AGATCTTTCTCTTTCAAGATTTGATCTTTC-TGAAGTAGGAGCAGAATAAGTCTA
66 GAAGCAGAATAAATCCCTCTCTTTCAAGATTTGATCTTCCTTG-AGTAACAGTGGAACAAGTCTA
246298 CCTCG
130 CCTCG
*
246303 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATCTGATTTTTCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATATGATTTTTCCTCAAGAA
* * * * *
246368 GAAGCAGAATAAATCCATCTCTTTCAAGATTTGATCTTCCCTGAGTAACAGCGGAATAAGTCTGC
66 GAAGCAGAATAAATCCCTCTCTTTCAAGATTTGATCTTCCTTGAGTAACAGTGGAACAAGTCTAC
*
246433 CTTG
131 CTCG
* * * ** * *
246437 ATTCAATCTTCCCTAAAAAATAGTGGAATGAATCAACATTTCCAGATAT-AATTTTCTCTTAAGA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATATGATTTTTC-CTCAAGA
* ** * * * * *
246501 AGCAGTGGAATAGATCCCTCTCTTTCCAGATTTGATCTTTCTTGAGTAACAGTAGAACAAGTCTG
65 AGAAGCAGAATAAATCCCTCTCTTTCAAGATTTGATCTTCCTTGAGTAACAGTGGAACAAGTCTA
246566 CCTCG
130 CCTCG
*
246571 ATTAAATCTTCCCTGAAGAACAGTG
1 ATTCAATCTTCCCTGAAGAACAGTG
246596 AGTCAACGTT
Statistics
Matches: 469, Mismatches: 78, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
129 1 0.00
130 111 0.24
131 1 0.00
133 117 0.25
134 237 0.51
135 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (134 bp):
ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATATGATTTTTCCTCAAGAA
GAAGCAGAATAAATCCCTCTCTTTCAAGATTTGATCTTCCTTGAGTAACAGTGGAACAAGTCTAC
CTCG
Found at i:246393 original size:264 final size:267
Alignment explanation
Indices: 245931--246595 Score: 786
Period size: 264 Copynumber: 2.5 Consensus size: 267
245921 AAGAGTAGTA
* * * * * * * *
245931 GAATAAATCAACATTCCCAGATCTGATTTTCCCTCAAGAAGAAGCAGAATATATCACTCTCTTTC
1 GAATGAATCAACATCCCCAGATATAATTTTCTCTCAAGAAGCAG-AGAATAGATCCCTCTCTTTC
* * * * *** *
245996 AAGATTTGATATTCCTTGAGGAATATTGGAACAAATC-AGCCTCGATTCAATCTT-CCTGAAGAA
65 AAGATTTGATCTTTCTTGAGTAACAGCAGAACAAGTCTA-CCTCGATTCAATCTTCCCTGAAGAA
* * ** * *
246059 CAGTGGAATGAATCAACGTCCCCAGATATGGTTTTCCCTCAAGAAGAAGTGGAACAAATCCCTTT
129 CAGTGGAATGAATCAACATCCCCAGATATGATTTTCCCTCAAGAAGAAGCAGAACAAATCCATCT
* *
246124 CTTTCAAGATTTGATCTTCCTTAAGTAACAGTGGAACAAGTCTAACTCGATTCAATCTTCCCTAA
194 CTTTCAAGATTTGATCTTCCCTAAGTAACAGCGGAACAAGTCTAACTCGATTCAATCTTCCCTAA
*
246189 AGAACAGTG
259 AAAACAGTG
* * * **
246198 GAATGAATCAACATCCCCAGATTTTATTTT-TGCTCAAGAAG-A-AGCA-AGATCTTTCTCTTTC
1 GAATGAATCAACATCCCCAGATATAATTTTCT-CTCAAGAAGCAGAGAATAGATCCCTCTCTTTC
** *
246259 AAGATTTGATCTTTC-TGAAGTAGGAGCAGAATAAGTCTACCTCGATTCAATCTTCCCTGAAGAA
65 AAGATTTGATCTTTCTTG-AGTAACAGCAGAACAAGTCTACCTCGATTCAATCTTCCCTGAAGAA
* * *
246323 CAGTGGAATGAATCAACATCCCCAGATCTGATTTTTCCTCAAGAAGAAGCAGAATAAATCCATCT
129 CAGTGGAATGAATCAACATCCCCAGATATGATTTTCCCTCAAGAAGAAGCAGAACAAATCCATCT
* * ** *
246388 CTTTCAAGATTTGATCTTCCCTGAGTAACAGCGGAATAAGTCTGCCTTGATTCAATCTTCCCTAA
194 CTTTCAAGATTTGATCTTCCCTAAGTAACAGCGGAACAAGTCTAACTCGATTCAATCTTCCCTAA
*
246453 AAAATAGTG
259 AAAACAGTG
** * *
246462 GAATGAATCAACATTTCCAGATATAATTTTCTCTTAAGAAGCAGTGGAATAGATCCCTCTCTTTC
1 GAATGAATCAACATCCCCAGATATAATTTTCTCTCAAGAAGCAG-AGAATAGATCCCTCTCTTTC
* * * *
246527 CAGATTTGATCTTTCTTGAGTAACAGTAGAACAAGTCTGCCTCGATTAAATCTTCCCTGAAGAAC
65 AAGATTTGATCTTTCTTGAGTAACAGCAGAACAAGTCTACCTCGATTCAATCTTCCCTGAAGAAC
246592 AGTG
130 AGTG
246596 AGTCAACGTT
Statistics
Matches: 335, Mismatches: 53, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
262 2 0.01
263 51 0.15
264 168 0.50
265 2 0.01
266 1 0.00
267 37 0.11
268 72 0.21
269 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (267 bp):
GAATGAATCAACATCCCCAGATATAATTTTCTCTCAAGAAGCAGAGAATAGATCCCTCTCTTTCA
AGATTTGATCTTTCTTGAGTAACAGCAGAACAAGTCTACCTCGATTCAATCTTCCCTGAAGAACA
GTGGAATGAATCAACATCCCCAGATATGATTTTCCCTCAAGAAGAAGCAGAACAAATCCATCTCT
TTCAAGATTTGATCTTCCCTAAGTAACAGCGGAACAAGTCTAACTCGATTCAATCTTCCCTAAAA
AACAGTG
Found at i:249043 original size:131 final size:130
Alignment explanation
Indices: 248788--249156 Score: 400
Period size: 131 Copynumber: 2.8 Consensus size: 130
248778 CTATATTGAG
* * * ** *
248788 AATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGAATGTTTTAAGGCATGAAAGAACATT
1 AATAATAACATCTCTTCATTTCAATTGGAGTAATAAATGAATGTTTTAAGGCATGAAAGATCATT
* * * * * *
248853 TATTCTTGATCGGAAATAATTTGATATTA-CTGATTTCTCTCGAATCAATATTGATTTTTAAGAC
66 TATTCTT-ATTGGAAATAATTAGATATTATC-GATTTCTCTCCAATCAATATTAAATTTTAAAAC
248917 GA
129 GA
* * * * * * *
248919 AATAATGACATCTCTTCATTTCAATTGGAGCAATAAATGAATGCTTTAAGGAATGAGAGGTTATT
1 AATAATAACATCTCTTCATTTCAATTGGAGTAATAAATGAATGTTTTAAGGCATGAAAGATCATT
* * * * * *
248984 TATTCTTATTTGAAAATCATTAGTTATTATCGTTTTCACTCCAATCGATATTAAATTTTAAAACG
66 TATTCTTA-TTGGAAATAATTAGATATTATCGATTTCTCTCCAATCAATATTAAATTTTAAAACG
249049 A
130 A
* * * *
249050 AATACTAATATCTCTTCATTTCAATTGG-GTTAATAAATGACTATTTTAAGGCATGAAAGATCAT
1 AATAATAACATCTCTTCATTTCAATTGGAG-TAATAAATGAATGTTTTAAGGCATGAAAGATCAT
* *
249114 TTATTCTCGATTGGAAATAATTAGATATTATCGCTTTCTCTCC
65 TTATTCT-TATTGGAAATAATTAGATATTATCGATTTCTCTCC
249157 TAAAATTATT
Statistics
Matches: 192, Mismatches: 42, Indels: 8
0.79 0.17 0.03
Matches are distributed among these distances:
130 2 0.01
131 188 0.98
132 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (130 bp):
AATAATAACATCTCTTCATTTCAATTGGAGTAATAAATGAATGTTTTAAGGCATGAAAGATCATT
TATTCTTATTGGAAATAATTAGATATTATCGATTTCTCTCCAATCAATATTAAATTTTAAAACGA
Found at i:251858 original size:120 final size:120
Alignment explanation
Indices: 251706--251947 Score: 466
Period size: 120 Copynumber: 2.0 Consensus size: 120
251696 TCCCGTGGCG
251706 ATCGGTATTTGATTTAGGGAGGATGGTTAATTTAATTTTTTGATTAATTATTTATTTCCTGATTG
1 ATCGGTATTTGATTTAGGGAGGATGGTTAATTTAATTTTTTGATTAATTATTTATTTCCTGATTG
251771 TATTCATCTTGAAATTTTATTTCTGTCAACTTTATATAAAAATTTTGTGTTGTTA
66 TATTCATCTTGAAATTTTATTTCTGTCAACTTTATATAAAAATTTTGTGTTGTTA
*
251826 ATCGGTGTTTGATTTAGGGAGGATGGTTAATTTAATTTTTTGATTAATTATTTATTTCCTGATTG
1 ATCGGTATTTGATTTAGGGAGGATGGTTAATTTAATTTTTTGATTAATTATTTATTTCCTGATTG
*
251891 TATTTATCTTGAAATTTTATTTCTGTCAACTTTATATAAAAATTTTGTGTTGTTA
66 TATTCATCTTGAAATTTTATTTCTGTCAACTTTATATAAAAATTTTGTGTTGTTA
251946 AT
1 AT
251948 ATGTATACAC
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.52
Consensus pattern (120 bp):
ATCGGTATTTGATTTAGGGAGGATGGTTAATTTAATTTTTTGATTAATTATTTATTTCCTGATTG
TATTCATCTTGAAATTTTATTTCTGTCAACTTTATATAAAAATTTTGTGTTGTTA
Found at i:257451 original size:21 final size:21
Alignment explanation
Indices: 257425--257485 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
257415 GTTAAGAGTC
257425 TTATTAGTTTGTTATGGTTTG
1 TTATTAGTTTGTTATGGTTTG
* *
257446 TTATTAGCTTGTTATTAG-TTG
1 TTATTAGTTTGTTA-TGGTTTG
*
257467 TTTTTAGTTTGTTATGGTT
1 TTATTAGTTTGTTATGGTT
257486 GTTGGTTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.15, C:0.02, G:0.21, T:0.62
Consensus pattern (21 bp):
TTATTAGTTTGTTATGGTTTG
Found at i:257457 original size:11 final size:11
Alignment explanation
Indices: 257425--257481 Score: 73
Period size: 11 Copynumber: 5.4 Consensus size: 11
257415 GTTAAGAGTC
257425 TTATTAGTTTG
1 TTATTAGTTTG
*
257436 TTA-TGGTTTG
1 TTATTAGTTTG
*
257446 TTATTAGCTTG
1 TTATTAGTTTG
257457 TTATTAG-TTG
1 TTATTAGTTTG
*
257467 TTTTTAGTTTG
1 TTATTAGTTTG
257478 TTAT
1 TTAT
257482 GGTTGTTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
10 18 0.46
11 21 0.54
ACGTcount: A:0.16, C:0.02, G:0.19, T:0.63
Consensus pattern (11 bp):
TTATTAGTTTG
Found at i:262007 original size:35 final size:34
Alignment explanation
Indices: 261922--262050 Score: 120
Period size: 35 Copynumber: 3.6 Consensus size: 34
261912 ATTTTTGTAA
* * * *
261922 TATATGTTATGTAGTTTTTAAAACGTTTTTGAAATCT
1 TATATATTATATAG-TTTTAAAAC-ATTTTGAAA-AT
261959 TATATATAATATATAAGTTTTAAAACATTTTGAAAAT
1 TATATAT--TATAT-AGTTTTAAAACATTTTGAAAAT
*
261996 TATATATTATATAGTTTTGAAATCATTTTGAAAA-
1 TATATATTATATAGTTTT-AAAACATTTTGAAAAT
262030 TATA-A-TATATAGTTTTTAAAA
1 TATATATTATATAG-TTTTAAAA
262051 AAATATGTTT
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
32 10 0.12
33 5 0.06
34 10 0.12
35 19 0.23
37 14 0.17
38 8 0.10
39 13 0.16
40 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (34 bp):
TATATATTATATAGTTTTAAAACATTTTGAAAAT
Found at i:262039 original size:32 final size:31
Alignment explanation
Indices: 261962--262187 Score: 131
Period size: 35 Copynumber: 6.7 Consensus size: 31
261952 GAAATCTTAT
261962 ATATAATATATAAGTTTTAAAACATTTTGAAA
1 ATATAATATAT-AGTTTTAAAACATTTTGAAA
*
261994 ATTATATATTATATAGTTTTGAAATCATTTTGAAA
1 A-TATA-A-TATATAGTTTT-AAAACATTTTGAAA
*
262029 ATATAATATATAGTTTTTAAAAAAATATGTTTTGAAA
1 ATATAATATATAG-TTTT---AAAACA--TTTTGAAA
262066 ATTTGTATAATATATAGTTTTAAAAAAACATTTTGGAAA
1 A----TATAATATATAGTTTT---AAAACATTTT-GAAA
*
262105 A-CT--TATAT--TTTTAAAATCATTTTTGAAAA
1 ATATAATATATAGTTTTAAAA-CA-TTTTG-AAA
* *
262134 CTATATAATATATAGTTTTCAAAACGTTTT-TAA
1 --ATATAATATATAGTTTT-AAAACATTTTGAAA
*
262167 ATATAATATATAGTTTAAAAA
1 ATATAATATATAGTTTTAAAA
262188 AATATTTGTT
Statistics
Matches: 159, Mismatches: 10, Indels: 52
0.72 0.05 0.24
Matches are distributed among these distances:
27 4 0.03
28 3 0.02
29 7 0.04
30 8 0.05
31 17 0.11
32 14 0.09
33 11 0.07
34 17 0.11
35 27 0.17
36 5 0.03
37 13 0.08
38 4 0.03
39 5 0.03
40 12 0.08
41 12 0.08
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (31 bp):
ATATAATATATAGTTTTAAAACATTTTGAAA
Found at i:262039 original size:39 final size:37
Alignment explanation
Indices: 261919--262040 Score: 115
Period size: 39 Copynumber: 3.2 Consensus size: 37
261909 AATATTTTTG
* * * *
261919 TAATATATGTTATGTAGTTTTTAAAACGTTTTTGAAATC
1 TAATATATATTATATAG-TTTTAAAAC-ATTTTGAAATA
* *
261958 TTATATATAATATATAAGTTTTAAAACATTTTGAAA-A
1 TAATATATATTATAT-AGTTTTAAAACATTTTGAAATA
*
261995 T--TATATATTATATAGTTTTGAAATCATTTTGAAAATA
1 TAATATATATTATATAGTTTT-AAAACATTTTG-AAATA
262032 TAATATATA
1 TAATATATA
262041 GTTTTTAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
34 6 0.09
35 21 0.30
36 3 0.04
37 3 0.04
38 8 0.12
39 26 0.38
40 2 0.03
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (37 bp):
TAATATATATTATATAGTTTTAAAACATTTTGAAATA
Found at i:262115 original size:29 final size:30
Alignment explanation
Indices: 262076--262140 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
262066 ATTTGTATAA
262076 TATATAGTTTTAAAAAAACATTTTGGAAAAC
1 TATATAGTTTT-AAAAAACATTTTGGAAAAC
* * *
262107 T-TATA-TTTTTAAAATCATTTTTGAAAAC
1 TATATAGTTTTAAAAAACATTTTGGAAAAC
262135 TATATA
1 TATATA
262141 ATATATAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 17 0.57
29 8 0.27
30 4 0.13
31 1 0.03
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (30 bp):
TATATAGTTTTAAAAAACATTTTGGAAAAC
Found at i:262249 original size:5 final size:5
Alignment explanation
Indices: 262239--262309 Score: 54
Period size: 5 Copynumber: 13.6 Consensus size: 5
262229 ATTATTAATA
* * * *
262239 TTTAT TTTAT TTTAT TTTAT TTCAT TTTAT TAATCTAA TTTAA TTTAA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T--T-TAT TTTAT TTTAT
*
262287 TTTAGT TTCA- TTTAT TTTAT TTT
1 TTTA-T TTTAT TTTAT TTTAT TTT
262310 TGTCAGGGTC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
4 3 0.05
5 44 0.80
6 4 0.07
7 1 0.02
8 3 0.05
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (5 bp):
TTTAT
Found at i:263334 original size:24 final size:23
Alignment explanation
Indices: 263307--263367 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
263297 AATAATATAT
*
263307 TTTTTATTT-TTTCTTCATTTTTTA
1 TTTTTATTTATTTCTTCA--ATTTA
*
263331 TTTTCATTTTATTTCTTCAATTTA
1 TTTTTA-TTTATTTCTTCAATTTA
263355 TTTTTATTTATTT
1 TTTTTATTTATTT
263368 ACCTTTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 7 0.22
24 14 0.44
25 3 0.09
26 8 0.25
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTTATTTATTTCTTCAATTTA
Found at i:263349 original size:13 final size:13
Alignment explanation
Indices: 263316--263357 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
263306 TTTTTTATTT
263316 TTTCTTCATTTT-
1 TTTCTTCATTTTA
*
263328 TTATTTTCATTTTA
1 TT-TCTTCATTTTA
*
263342 TTTCTTCAATTTA
1 TTTCTTCATTTTA
263355 TTT
1 TTT
263358 TTATTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCTTCATTTTA
Found at i:263463 original size:27 final size:28
Alignment explanation
Indices: 263433--263489 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
263423 TTATTTACTA
263433 TTATATTTTTACTTTTATTT-TATGTTT
1 TTATATTTTTACTTTTATTTATATGTTT
* * *
263460 TTATGTTTTTATTTTTATTTATTTGTTT
1 TTATATTTTTACTTTTATTTATATGTTT
263488 TT
1 TT
263490 CTATCTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (28 bp):
TTATATTTTTACTTTTATTTATATGTTT
Found at i:265186 original size:19 final size:19
Alignment explanation
Indices: 265159--265195 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
265149 ATTTAGACGT
265159 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
*
265178 TTTGTATTTTGTTATTTT
1 TTTGCATTTTGTTATTTT
265196 TCCTTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.05, G:0.11, T:0.73
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:266450 original size:84 final size:83
Alignment explanation
Indices: 266209--267096 Score: 753
Period size: 84 Copynumber: 10.7 Consensus size: 83
266199 ACTCAAGGCT
** * *
266209 AGAAGGGTTATCTGTGACCAAAA-ACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATT
*
266273 TGCAGCATATCTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* * * * *
266292 AGAA-GATCTATCTGCCAAC----GACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCA
1 AGAAGGGT-TATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TC-AAGGCACATCA
* * * * *
266352 TCTGCAGTACAACTTAACTCT
63 TTTGCAGCATAACTTAAGTCG
* * * *
266373 AGAAGGGTTGTTTGCCAACAAAAGAACTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCACATCATT
*
266438 TGCAGAATAACTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* * * * * *
266457 AGAAGGGCTATCTG-C--C-AAAGACCCTCGAGTTTGATTACGCTCAGCTTCGAGGGCTCATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TC-AAGGCACATCAT
* * * *
266518 TTACAGCATAACTCAAGGCT
64 TTGCAGCATAACTTAAGTCG
* * * *
266538 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACTCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATT
* * * * *
266603 TGCAACATAGCTCAAGGCA
65 TGCAGCATAACTTAAGTCG
* * * * *
266622 AGAAGGGTTATTTGCCAATAAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATT
** * *
266687 TATAGCATAACTTAAATCA
65 TGCAGCATAACTTAAGTCG
* * * * *
266706 AGAAGGGTTATATGTCACCAAAAGACCTTCAAGTTCGACTACGCTCAGCTCCGAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATT
* * *
266771 TGTAGCATAGCTTAAGTTG
65 TGCAGCATAACTTAAGTCG
* * * * * *
266790 AGAAGGGTTAT-TG-C--C-AAAGACCCTCAAGTTCGATTACACTCAGCTTTGAGGGCACATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC--TCAAGGCACATCAT
* * * * *
266850 TTACATCATAACTCAAGGCT
64 TTGCAGCATAACTTAAGTCG
* * * * * * * ** *
266870 AGAAGGGTTATCTGTCACCAAAAGACCTTCAACTTCGATTACACTCAGCTTCGAGGGTGCATCTT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TC-AAGGCACATCAT
266935 TTGCAGCATAACTTAAGTCG
64 TTGCAGCATAACTTAAGTCG
*
266955 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATT
* * *
267020 TGTAACATAGCTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* ** * *
267039 AGAAGGGCTATCTGCCAACCGAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC-AAGGCA
267097 AACCAAATTT
Statistics
Matches: 649, Mismatches: 129, Indels: 53
0.78 0.16 0.06
Matches are distributed among these distances:
79 26 0.04
80 80 0.12
81 82 0.13
82 8 0.01
83 17 0.03
84 296 0.46
85 140 0.22
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTT
GCAGCATAACTTAAGTCG
Found at i:266510 original size:165 final size:165
Alignment explanation
Indices: 266199--267096 Score: 928
Period size: 165 Copynumber: 5.4 Consensus size: 165
266189 AAGGCTTCAT
* *
266199 ACTCAAGGCTAGAAGGGTTATCTGTGACCAAAA-ACCTTCGAGTTCGACTATGCTCAGCTCCAAG
1 ACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
* * *
266263 GCACATCATTTGCAGCATATCTTAAGTCGAGAA-GATCTATCTGCCAACGACCCTCGAGTTCGAT
66 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGT-TATCTGCCAAAGACCCTCGAGTTCGAT
* * * * *
266327 TACACTCAGCTTCGAGGGCACATCATCTGCAGTACA
130 TACGCTCAGCTTCGAGGGCACATCATTTACAGCATA
* ** * * * * * *
266363 ACTTAACTCTAGAAGGGTTGTTTGCCAACAAAAGAACTTTGAGTTCGACTACGCTCAGCT-CAAC
1 ACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-
* * *
266427 GGCACATCATTTGCAGAATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGAT
65 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGAT
*
266492 TACGCTCAGCTTCGAGGGCTCATCATTTACAGCATA
130 TACGCTCAGCTTCGAGGGCACATCATTTACAGCATA
* *
266528 ACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACTCTCAGCTCCAAG
1 ACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
* * * * * * * *
266593 GCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAATAAAAGACCTTCGAGTTT
66 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC----AAAGACCCTCGAGTTC
* * * * * *
266658 GACTACGTTCAGC-TCCAAGGCATATCATTTATAGCATA
127 GATTACGCTCAGCTTCGAGGGCACATCATTTACAGCATA
* ** * * * *
266696 ACTTAAATCAAGAAGGGTTATATGTCACCAAAAGACCTTCAAGTTCGACTACGCTCAGCTCCGAG
1 ACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
* * * *
266761 GCACATCATTTGTAGCATAGCTTAAGTTGAGAAGGGTTAT-TGCCAAAGACCCTCAAGTTCGATT
66 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATT
* * *
266825 ACACTCAGCTTTGAGGGCACATCATTTACATCATA
131 ACGCTCAGCTTCGAGGGCACATCATTTACAGCATA
* * * * * *
266860 ACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCAACTTCGATTACACTCAGCTTCGAG
1 ACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAA
** * *
266925 GGTGCATCTTTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
65 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG----CCAAAGACCCTCGAGTT
* * * ** *
266990 CGACTACGCTCAGC-TCCAAGGCACATCATTTGTAACATA
126 CGATTACGCTCAGCTTCGAGGGCACATCATTTACAGCATA
* * * * * * * * * *
267029 GCTTAAGTCGAGAAGGGCTATCTGCCAACC-GAAGACCTTCGAGTTCGATTACACTCAGCTCAAA
1 ACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
267093 GGCA
65 GGCA
267097 AACCAAATTT
Statistics
Matches: 601, Mismatches: 117, Indels: 28
0.81 0.16 0.04
Matches are distributed among these distances:
163 23 0.04
164 98 0.16
165 234 0.39
166 6 0.01
167 4 0.01
168 115 0.19
169 91 0.15
170 30 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (165 bp):
ACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATT
ACGCTCAGCTTCGAGGGCACATCATTTACAGCATA
Found at i:266981 original size:333 final size:333
Alignment explanation
Indices: 266195--267089 Score: 1081
Period size: 333 Copynumber: 2.7 Consensus size: 333
266185 CCTGAAGGCT
* **
266195 TCAT-ACTCAAGGCTAGAAGGGTTATCTGTGACCAAAA-ACCTTCGAGTTCGACTATGCTCAGCT
1 TCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACACTCAGCT
* * *
266258 CCAAGGCACATCATTTGCAGCATATCTTAAGTCGAGAA-GATCTATCTGCCAAC---GACCCTCG
66 CCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGT-TATCTGCCAACAAAGACCTTCG
* * * * * * * * * * *
266319 AGTTCGATTACACTCAGCTTCGAGGGCACATCATCTGCAGTACAACTTAACTCTAGAAGGGTTGT
130 AGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGTAGCATAACTTAAATCAAGAAGGGTTAT
* * * *
266384 TTGCCAACAAAAGAACTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGAATAA
194 ATGCCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAACGGCACATCATTTGCAGAATAA
* * * *
266448 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACGCTCAGCTTCGAGGGCTC
259 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCAC
266513 ATCATTTACA
324 ATCATTTACA
* * *
266523 GCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACTCTCAGCT
1 TCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACACTCAGCT
* * * * * * *
266588 CCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAATAAAAGACCTTCG
66 CCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCG
* * * *
266653 AGTTTGACTACGTTCAGCTCCAAGGCATATCATTTATAGCATAACTTAAATCAAGAAGGGTTATA
130 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAACTTAAATCAAGAAGGGTTATA
* * * * * *
266718 TGTCACCAAAAGACCTTCAAGTTCGACTACGCTCAGCTCCGA-GGCACATCATTTGTAGCATAGC
195 TGCCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAACGGCACATCATTTGCAGAATAAC
* * *
266782 TTAAGTTGAGAAGGGTTAT-TGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTTGAGGGCACA
260 TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACA
266846 TCATTTACA
325 TCATTTACA
* * *
266855 TCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCAACTTCGATTACACTCAGCT
1 TCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACACTCAGC-
* * ** *
266920 TCGAGGGTGCATCTTTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTC
65 TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTC
* * * * *
266985 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAACATAGCTTAAGTCGAGAAGGGCTAT
129 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAACTTAAATCAAGAAGGGTTAT
* * * *
267050 CTGCCAACC-GAAGACCTTCGAGTTCGATTACACTCAGCTC
194 ATGCC-ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
267090 AAAGGCAAAC
Statistics
Matches: 477, Mismatches: 80, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
328 3 0.01
329 32 0.07
330 65 0.14
331 2 0.00
332 107 0.22
333 242 0.51
334 26 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (333 bp):
TCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACACTCAGCT
CCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGA
GTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAACTTAAATCAAGAAGGGTTATAT
GCCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAACGGCACATCATTTGCAGAATAACT
TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
CATTTACA
Found at i:267839 original size:35 final size:31
Alignment explanation
Indices: 267787--267858 Score: 99
Period size: 35 Copynumber: 2.2 Consensus size: 31
267777 ACAATACATA
267787 AGTTTTAAAACATTTTGAAAATTATATAGTATAT
1 AGTTTTAAAACATTTTGAAAA-TATA-A-TATAT
*
267821 AGTTTTGAAATCATTTTGAAAATATAATATAT
1 AGTTTT-AAAACATTTTGAAAATATAATATAT
267853 AGTTTT
1 AGTTTT
267859 TTAAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
32 11 0.31
33 1 0.03
34 10 0.28
35 14 0.39
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.46
Consensus pattern (31 bp):
AGTTTTAAAACATTTTGAAAATATAATATAT
Found at i:271320 original size:23 final size:21
Alignment explanation
Indices: 271271--271352 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
271261 ACAGAACCCC
* *
271271 AAGGGGGTATCGATTCCCCTGT
1 AAGGGGGGATCGGTTCCCCT-T
*
271293 -GGGGGGGATCGGTTCCCCTT
1 AAGGGGGGATCGGTTCCCCTT
*
271313 CAAAGGGGGAATCGGTT-CCCTT
1 --AAGGGGGGATCGGTTCCCCTT
* *
271335 ATGGGGGGATCGATTCCC
1 AAGGGGGGATCGGTTCCC
271353 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
20 13 0.27
21 18 0.38
22 5 0.10
23 12 0.25
ACGTcount: A:0.16, C:0.23, G:0.37, T:0.24
Consensus pattern (21 bp):
AAGGGGGGATCGGTTCCCCTT
Found at i:271343 original size:21 final size:20
Alignment explanation
Indices: 271273--271353 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
271263 AGAACCCCAA
* * *
271273 GGGGGTATCGATTCCCCTGT
1 GGGGGGATCGATTCCCTTAT
* *
271293 GGGGGGGATCGGTTCCCCTTCAAA
1 -GGGGGGATCGATT-CCCTT--AT
* *
271317 GGGGGAATCGGTTCCCTTAT
1 GGGGGGATCGATTCCCTTAT
271337 GGGGGGATCGATTCCCT
1 GGGGGGATCGATTCCCT
271354 CTGCACCAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
20 16 0.33
21 11 0.23
22 9 0.19
23 12 0.25
ACGTcount: A:0.14, C:0.23, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTTAT
Found at i:277555 original size:24 final size:23
Alignment explanation
Indices: 277497--277556 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
277487 AAATATTATA
*
277497 TTTTTAAA-ATCATTTTTGAAAAC
1 TTTTTAAATAT-AGTTTTGAAAAC
* *
277520 TATATAATATATAGTTTTGAAAAC
1 TTTTTAA-ATATAGTTTTGAAAAC
277544 GTTTTTAAATATA
1 -TTTTTAAATATA
277557 ATATATAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 5 0.17
24 17 0.59
25 7 0.24
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (23 bp):
TTTTTAAATATAGTTTTGAAAAC
Found at i:277634 original size:10 final size:9
Alignment explanation
Indices: 277616--277677 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
277606 TTATTATTAA
277616 TATTTATTT
1 TATTTATTT
277625 TATTTCATTT
1 TATTT-ATTT
* *
277635 TATTAATCT
1 TATTTATTT
*
277644 AATTTAATTT
1 TATTT-ATTT
*
277654 AATTTAGTTT
1 TATTTA-TTT
*
277664 CATTTATTT
1 TATTTATTT
277673 TATTT
1 TATTT
277678 TTGTCAGGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
9 19 0.44
10 24 0.56
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (9 bp):
TATTTATTT
Found at i:277636 original size:15 final size:14
Alignment explanation
Indices: 277617--277677 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 14
277607 TATTATTAAT
277617 ATTTATTTTATTTC
1 ATTTATTTTATTTC
*
277631 ATTTTATTAATCTAATTTA
1 A-TTTATT--T-T-ATTTC
*
277650 ATTTAATTTAGTTTC
1 ATTTATTTTA-TTTC
277665 ATTTATTTTATTT
1 ATTTATTTTATTT
277678 TTGTCAGGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
14 5 0.14
15 19 0.51
16 1 0.03
17 1 0.03
18 6 0.16
19 5 0.14
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (14 bp):
ATTTATTTTATTTC
Found at i:278599 original size:23 final size:23
Alignment explanation
Indices: 278573--278641 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
278563 CACCACAGCT
*
278573 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
278596 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
278619 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
278642 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:283916 original size:23 final size:23
Alignment explanation
Indices: 283890--283955 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
283880 CAGCTCGTAT
283890 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
* * * **
283913 AATTGCCTCCGGAGTGTCGCGTAG
1 AATTG-CACCGAAGTGCCATGTAG
*
283937 AATTGCACCGTAGTGCCAT
1 AATTGCACCGAAGTGCCAT
283956 ATAATAATGT
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:286649 original size:17 final size:17
Alignment explanation
Indices: 286629--286715 Score: 68
Period size: 17 Copynumber: 4.9 Consensus size: 17
286619 TAAAATAATA
286629 TTTTTTTTATTTTTTAT
1 TTTTTTTTATTTTTTAT
* **
286646 TTTTCTTCCTTTTTTA-
1 TTTTTTTTATTTTTTAT
* *
286662 TTTTATTTCTTTTTTAT
1 TTTTTTTTATTTTTTAT
*
286679 TTTTATTTTATTTCTTCGAT
1 TTTT-TTTTATTT-TT-TAT
*
286699 TTATTTTTATTTATTTA
1 TTTTTTTTATTT-TTTA
286716 CCTTTTTGTA
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
16 14 0.25
17 17 0.31
18 7 0.13
19 12 0.22
20 5 0.09
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.78
Consensus pattern (17 bp):
TTTTTTTTATTTTTTAT
Found at i:286658 original size:22 final size:21
Alignment explanation
Indices: 286633--286710 Score: 58
Period size: 22 Copynumber: 3.7 Consensus size: 21
286623 ATAATATTTT
286633 TTTTATTTTTTATTTTTCTTCC
1 TTTTATTTTTTATTTTTCTT-C
286655 TTTT-TTATTTTA--TTTCTT-
1 TTTTATT-TTTTATTTTTCTTC
*
286673 TTTTATTTTTATTTTATTTCTTC
1 TTTTATTTTT-TATT-TTTCTTC
*
286696 GATTTA-TTTTTATTT
1 -TTTTATTTTTTATTT
286711 ATTTACCTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 17
0.69 0.05 0.26
Matches are distributed among these distances:
18 7 0.16
19 3 0.07
20 6 0.13
21 3 0.07
22 18 0.40
23 4 0.09
24 4 0.09
ACGTcount: A:0.13, C:0.08, G:0.01, T:0.78
Consensus pattern (21 bp):
TTTTATTTTTTATTTTTCTTC
Found at i:286676 original size:11 final size:12
Alignment explanation
Indices: 286659--286714 Score: 59
Period size: 11 Copynumber: 4.9 Consensus size: 12
286649 TCTTCCTTTT
286659 TTATTTTATTTC
1 TTATTTTATTTC
286671 TT-TTTTATTT-
1 TTATTTTATTTC
286681 TTATTTTATTTC
1 TTATTTTATTTC
286693 TTCGA-TTTATTT-
1 TT--ATTTTATTTC
286705 TTA-TTTATTT
1 TTATTTTATTT
286715 ACCTTTTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.25
11 16 0.40
12 6 0.15
13 7 0.17
14 1 0.03
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (12 bp):
TTATTTTATTTC
Found at i:287932 original size:3 final size:3
Alignment explanation
Indices: 287917--288003 Score: 72
Period size: 3 Copynumber: 29.0 Consensus size: 3
287907 TTCGTATCTT
* * *
287917 ATA ATA AT- TTA ATA ATA ATA ATA ATA CTTA ATA AT- ATA ATA TATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA
* * *
287962 ATA TATA AAA ATA GTA ATA ATA GTA ATA ATA AT- ATA ATA ATA
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
288004 TCAACTCGGA
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
2 5 0.08
3 54 0.82
4 7 0.11
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:291893 original size:31 final size:31
Alignment explanation
Indices: 291853--291922 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
291843 TGGAAAGCAT
291853 GAAGACGTCGACTGTTCCAACCGTTTTCTAA
1 GAAGACGTCGACTGTTCCAACCGTTTTCTAA
*
291884 GAAGGCGTCGACTGTTCCAACCGTTTTCTAA
1 GAAGACGTCGACTGTTCCAACCGTTTTCTAA
291915 GAAGACGT
1 GAAGACGT
291923 TATGTGCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (31 bp):
GAAGACGTCGACTGTTCCAACCGTTTTCTAA
Found at i:293016 original size:17 final size:17
Alignment explanation
Indices: 292996--293077 Score: 51
Period size: 17 Copynumber: 4.6 Consensus size: 17
292986 TATATTAATG
292996 TATATATTATATGATAA
1 TATATATTATATGATAA
293013 TATA-ATATATATGATGAA
1 TATATAT-TATATGAT-AA
* *
293031 TGATATGATAATATAATACA
1 T-ATAT-ATTATATGATA-A
* *
293051 TGTATA-TATATTATAA
1 TATATATTATATGATAA
* *
293067 TGTACATTATA
1 TATATATTATA
293078 ATTATACATA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
16 8 0.15
17 23 0.44
18 4 0.08
19 7 0.13
20 8 0.15
21 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATTATATGATAA
Found at i:293179 original size:20 final size:21
Alignment explanation
Indices: 293163--293202 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
293153 ATAATATATA
293163 TATAC-TATAGTTTATATACT
1 TATACTTATAGTTTATATACT
293183 TATACTTTATAGTTTATATA
1 TATAC-TTATAGTTTATATA
293203 AAAGTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
TATACTTATAGTTTATATACT
Found at i:293180 original size:14 final size:15
Alignment explanation
Indices: 293161--293193 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
293151 ACATAATATA
*
293161 TATATAC-TATAGTT
1 TATATACTTATACTT
293175 TATATACTTATACTT
1 TATATACTTATACTT
293190 TATA
1 TATA
293194 GTTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (15 bp):
TATATACTTATACTT
Found at i:293228 original size:16 final size:16
Alignment explanation
Indices: 293197--293272 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
293187 CTTTATAGTT
*
293197 TATATAAAAGTATAAAA
1 TATAT-AAACTATAAAA
293214 TATATAAACTAT-AAA
1 TATATAAACTATAAAA
* *
293229 -ATATCAAGTCA-AAAA
1 TATATAAACT-ATAAAA
* *
293244 AATATAAACTATAAAC
1 TATATAAACTATAAAA
*
293260 TATATAAATTATA
1 TATATAAACTATA
293273 TAGTATATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
14 7 0.15
15 8 0.17
16 27 0.57
17 5 0.11
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (16 bp):
TATATAAACTATAAAA
Found at i:293293 original size:26 final size:26
Alignment explanation
Indices: 293260--293310 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
293250 AACTATAAAC
* * *
293260 TATATAAATTATATAGTATATGTATG
1 TATATAAACTATATAGCATAAGTATG
293286 TATATAAACTATATAGCATAAGTAT
1 TATATAAACTATATAGCATAAGTAT
293311 ATAAGTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (26 bp):
TATATAAACTATATAGCATAAGTATG
Found at i:293367 original size:42 final size:42
Alignment explanation
Indices: 293245--293367 Score: 108
Period size: 42 Copynumber: 2.9 Consensus size: 42
293235 AGTCAAAAAA
* * * *
293245 ATATAAACTATA-AAC-TATATAAATTATATAGTATATGTATGT
1 ATATAAACTATATAGCATAAATAAA-TATATA-TATATATAAGT
* * * *
293287 ATATAAACTATATAGCATAAGTATATA-AGTTTACATATAAGT
1 ATATAAACTATATAGCATAAATAAATATA-TATATATATAAGT
* *
293329 ATATAAACTATATGGTATAAATAAATATATATATATATA
1 ATATAAACTATATAGCATAAATAAATATATATATATATA
293368 TATGTATGTA
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
42 52 0.83
43 6 0.10
44 5 0.08
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (42 bp):
ATATAAACTATATAGCATAAATAAATATATATATATATAAGT
Found at i:293438 original size:15 final size:15
Alignment explanation
Indices: 293420--293450 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
293410 GCATAAGTAT
293420 ATATATAAGTATATA
1 ATATATAAGTATATA
293435 ATATATAAGTATATA
1 ATATATAAGTATATA
293450 A
1 A
293451 ACTATATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
ATATATAAGTATATA
Found at i:293447 original size:8 final size:8
Alignment explanation
Indices: 293421--293450 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
293411 CATAAGTATA
293421 TATATAAG
1 TATATAAG
293429 TATATAA-
1 TATATAAG
293436 TATATAAG
1 TATATAAG
293444 TATATAA
1 TATATAA
293451 ACTATATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (8 bp):
TATATAAG
Found at i:293456 original size:15 final size:14
Alignment explanation
Indices: 293412--293456 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
293402 AAACTATAGC
293412 ATAAGTATAT--AT
1 ATAAGTATATAAAT
293424 ATAAGTATATAATAT
1 ATAAGTATATAA-AT
293439 ATAAGTATATAAACT
1 ATAAGTATATAAA-T
293454 ATA
1 ATA
293457 TGGTATAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.34
14 1 0.03
15 18 0.62
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (14 bp):
ATAAGTATATAAAT
Found at i:293505 original size:11 final size:11
Alignment explanation
Indices: 293473--293550 Score: 77
Period size: 11 Copynumber: 6.9 Consensus size: 11
293463 AAGAATATAT
293473 ATGCATGTATG
1 ATGCATGTATG
**
293484 TATATATGTATG
1 -ATGCATGTATG
293496 ATGCATGTATG
1 ATGCATGTATG
*
293507 ATACATGTATG
1 ATGCATGTATG
**
293518 -TGTGTGTAATG
1 ATGCATGT-ATG
293529 CATGCATGTATG
1 -ATGCATGTATG
293541 ATGCATGTAT
1 ATGCATGTAT
293551 ATATATACAT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
10 4 0.08
11 32 0.60
12 12 0.23
13 5 0.09
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (11 bp):
ATGCATGTATG
Found at i:293515 original size:34 final size:36
Alignment explanation
Indices: 293476--293557 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 36
293466 AATATATATG
293476 CATGTATGTATATATGT-ATG-ATGCATGTATGATA
1 CATGTATGTATATATGTAATGCATGCATGTATGATA
* * *
293510 CATGTATG--TGTGTGTAATGCATGCATGTATGATG
1 CATGTATGTATATATGTAATGCATGCATGTATGATA
*
293544 CATGTATATATATA
1 CATGTATGTATATA
293558 CATATATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
32 5 0.13
33 3 0.08
34 28 0.74
36 2 0.05
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.40
Consensus pattern (36 bp):
CATGTATGTATATATGTAATGCATGCATGTATGATA
Found at i:293620 original size:2 final size:2
Alignment explanation
Indices: 293613--293652 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
293603 ATAATAGATG
*
293613 TA TA TA TA T- TA -A TA T- TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
293652 T
1 T
293653 GATGTATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:293686 original size:16 final size:15
Alignment explanation
Indices: 293665--293694 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
293655 TGTATGTACA
293665 TAAGTATATAAATATC
1 TAAGTATA-AAATATC
293681 TAAGTATAAAATAT
1 TAAGTATAAAATAT
293695 GTGTGTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (15 bp):
TAAGTATAAAATATC
Found at i:295371 original size:2 final size:2
Alignment explanation
Indices: 295364--295458 Score: 153
Period size: 2 Copynumber: 49.5 Consensus size: 2
295354 GAACACATTA
*
295364 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT CT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
295404 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
295444 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
295459 ATCAGAATAA
Statistics
Matches: 88, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
1 4 0.05
2 84 0.95
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:301669 original size:22 final size:22
Alignment explanation
Indices: 301627--301671 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
301617 ATGTTCATTT
*
301627 TACATAACTTAGAAACAAAAAA
1 TACATAACTTACAAACAAAAAA
*
301649 TACATAAC-TACAAATATAAAAA
1 TACATAACTTACAAACA-AAAAA
301671 T
1 T
301672 TTTATATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.22
Consensus pattern (22 bp):
TACATAACTTACAAACAAAAAA
Found at i:309360 original size:31 final size:31
Alignment explanation
Indices: 309324--309393 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
309314 TGGAAAGCAT
309324 GAAGACGTCGACTGTTCCAACCGTTTTCTAA
1 GAAGACGTCGACTGTTCCAACCGTTTTCTAA
309355 GAAGACGTCGACTGTTCCAACCGTTTTCTAA
1 GAAGACGTCGACTGTTCCAACCGTTTTCTAA
309386 GAAGACGT
1 GAAGACGT
309394 TATGTGCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (31 bp):
GAAGACGTCGACTGTTCCAACCGTTTTCTAA
Found at i:310623 original size:2 final size:2
Alignment explanation
Indices: 310618--310672 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
310608 ATATGTACTA
310618 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
310659 AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT A
310673 CTTATACTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:310628 original size:23 final size:20
Alignment explanation
Indices: 310618--310672 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 20
310608 ATATGTACTA
310618 ATATATATATATATATATAT
1 ATATATATATATATATATAT
310638 ATATAT-TATATATATATAT
1 ATATATATATATATATATAT
310657 ATATATATAT-TATATA
1 ATATATATATATATATA
310673 CTTATACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 25 0.74
20 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATATATATATATATAT
Found at i:310678 original size:23 final size:23
Alignment explanation
Indices: 310618--310678 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 23
310608 ATATGTACTA
310618 ATATATATATATA-TATATATAT
1 ATATATATATATATTATATATAT
310640 ATAT-TATATATA-TATATATAT
1 ATATATATATATATTATATATAT
310661 ATATAT-TATATACTTATA
1 ATATATATATATA-TTATA
310679 CTTTATAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 27 0.75
22 5 0.14
23 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATATATATATATTATATATAT
Found at i:310720 original size:16 final size:16
Alignment explanation
Indices: 310689--310764 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
310679 CTTTATAGTT
*
310689 TATATAAAAGTATAAAA
1 TATAT-AAACTATAAAA
310706 TATATAAACTAT-AAA
1 TATATAAACTATAAAA
* *
310721 -ATATCAAGTCA-AAAA
1 TATATAAACT-ATAAAA
* *
310736 AATATAAACTATAAAC
1 TATATAAACTATAAAA
*
310752 TATATAAATTATA
1 TATATAAACTATA
310765 TAGTATATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
14 7 0.15
15 8 0.17
16 27 0.57
17 5 0.11
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (16 bp):
TATATAAACTATAAAA
Found at i:310790 original size:35 final size:35
Alignment explanation
Indices: 310745--310811 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
310735 AAATATAAAC
* * *
310745 TATAAACTATATAAATTATATAGTATATGTATGTA
1 TATAAACTATATAAACTATATAGCATAAGTATGTA
310780 TATAAACTATATAAACTATATAGCATAAGTAT
1 TATAAACTATATAAACTATATAGCATAAGTAT
310812 ATAAGTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (35 bp):
TATAAACTATATAAACTATATAGCATAAGTATGTA
Found at i:310815 original size:22 final size:22
Alignment explanation
Indices: 310787--310869 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 22
310777 GTATATAAAC
*
310787 TATATAAACTATATAGCATAAG
1 TATATAAACTATATAGTATAAG
* * *
310809 TATAT-AAGTTTACA-TATAAG
1 TATATAAACTATATAGTATAAG
*
310829 TATATAAACTATATGGTATAAG
1 TATATAAACTATATAGTATAAG
*
310851 TATATATA-TATATATGTAT
1 TATATAAACTATATA-GTAT
310870 GTACATATGT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 10 0.21
21 16 0.33
22 22 0.46
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.40
Consensus pattern (22 bp):
TATATAAACTATATAGTATAAG
Found at i:310858 original size:101 final size:102
Alignment explanation
Indices: 310752--310963 Score: 272
Period size: 106 Copynumber: 2.0 Consensus size: 102
310742 AACTATAAAC
**
310752 TATATAAATTATATAGTA-TATGTATGTATATAAACTATATAAACTATATAGCATAAG-TATATA
1 TATATAAA-TATAT-GTAGTACATATGTATATAAACTATATAAAC--TATAGCATAAGATATATA
*
310815 AGT-T-T-ACATATAAGTATATAAACTATATGGTATAAGTA
62 AGTATATAACATATAAGTATATAAACTATATGGTATAAGAA
*
310853 TATATATATATATGTATGTACATATGTATATAAACTATATAAACTATAGCATAAGTATATATATA
1 TATATAAATATATGTA-GTACATATGTATATAAACTATATAAACTATAGCATAAG---ATATATA
*
310918 AGTATATAATATATAAGTATATAAACTATATGGTATAAGAA
62 AGTATATAACATATAAGTATATAAACTATATGGTATAAGAA
310959 TATAT
1 TATAT
310964 GCATGTATGT
Statistics
Matches: 97, Mismatches: 5, Indels: 13
0.84 0.04 0.11
Matches are distributed among these distances:
99 14 0.14
100 5 0.05
101 31 0.32
103 9 0.09
104 1 0.01
105 1 0.01
106 36 0.37
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (102 bp):
TATATAAATATATGTAGTACATATGTATATAAACTATATAAACTATAGCATAAGATATATAAGTA
TATAACATATAAGTATATAAACTATATGGTATAAGAA
Found at i:310894 original size:59 final size:56
Alignment explanation
Indices: 310829--310948 Score: 152
Period size: 56 Copynumber: 2.1 Consensus size: 56
310819 TACATATAAG
* * * *
310829 TATATAAACTATATGGTATAAGTATATATATATA-TATGTATGTACATATGTATATAAAC
1 TATATAAACTATA--GCATAAGTATATATATA-AGTATATA-ATACATAAGTATATAAAC
*
310888 TATATAAACTATAGCATAAGTATATATATAAGTATATAATATATAAGTATATAAAC
1 TATATAAACTATAGCATAAGTATATATATAAGTATATAATACATAAGTATATAAAC
310944 TATAT
1 TATAT
310949 GGTATAAGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
56 21 0.38
57 21 0.38
59 13 0.24
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (56 bp):
TATATAAACTATAGCATAAGTATATATATAAGTATATAATACATAAGTATATAAAC
Found at i:310929 original size:15 final size:15
Alignment explanation
Indices: 310911--310941 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
310901 GCATAAGTAT
310911 ATATATAAGTATATA
1 ATATATAAGTATATA
310926 ATATATAAGTATATA
1 ATATATAAGTATATA
310941 A
1 A
310942 ACTATATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
ATATATAAGTATATA
Found at i:310938 original size:8 final size:8
Alignment explanation
Indices: 310912--310941 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
310902 CATAAGTATA
310912 TATATAAG
1 TATATAAG
310920 TATATAA-
1 TATATAAG
310927 TATATAAG
1 TATATAAG
310935 TATATAA
1 TATATAA
310942 ACTATATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (8 bp):
TATATAAG
Found at i:310947 original size:15 final size:14
Alignment explanation
Indices: 310903--310947 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
310893 AAACTATAGC
310903 ATAAGTATAT--AT
1 ATAAGTATATAAAT
310915 ATAAGTATATAATAT
1 ATAAGTATATAA-AT
310930 ATAAGTATATAAACT
1 ATAAGTATATAAA-T
310945 ATA
1 ATA
310948 TGGTATAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.34
14 1 0.03
15 18 0.62
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (14 bp):
ATAAGTATATAAAT
Found at i:310962 original size:106 final size:100
Alignment explanation
Indices: 310774--310963 Score: 283
Period size: 106 Copynumber: 1.8 Consensus size: 100
310764 ATAGTATATG
310774 TATGTATATAAACTATATAAACTATATAGCATAAGTATATAAGTTTACATATAAGTATATAAACT
1 TATGTATATAAACTATATAAAC-ATATAGCATAAGTATATAAGTTTACATATAAGTATATAAACT
*
310839 ATATGGTATAAGTATATATATATATATGTATGTACA
65 ATATGGTATAAGAATATATATATATATGTATGTACA
*
310875 TATGTATATAAACTATATAAAC-TATAGCATAAGTATATATATAAGTATATAATATATAAGTATA
1 TATGTATATAAACTATATAAACATATAGCATAAG----TATATAAGT-T-T-ACATATAAGTATA
310939 TAAACTATATGGTATAAGAATATAT
59 TAAACTATATGGTATAAGAATATAT
310964 GCATGTATGT
Statistics
Matches: 80, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
99 11 0.14
101 22 0.28
103 9 0.11
104 1 0.01
105 1 0.01
106 36 0.45
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.38
Consensus pattern (100 bp):
TATGTATATAAACTATATAAACATATAGCATAAGTATATAAGTTTACATATAAGTATATAAACTA
TATGGTATAAGAATATATATATATATGTATGTACA
Found at i:310994 original size:11 final size:11
Alignment explanation
Indices: 310962--311039 Score: 77
Period size: 11 Copynumber: 6.9 Consensus size: 11
310952 ATAAGAATAT
310962 ATGCATGTATG
1 ATGCATGTATG
**
310973 TATATATGTATG
1 -ATGCATGTATG
310985 ATGCATGTATG
1 ATGCATGTATG
*
310996 ATACATGTATG
1 ATGCATGTATG
**
311007 -TGTGTGTAATG
1 ATGCATGT-ATG
311018 CATGCATGTATG
1 -ATGCATGTATG
311030 ATGCATGTAT
1 ATGCATGTAT
311040 ATATATACAT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
10 4 0.08
11 32 0.60
12 12 0.23
13 5 0.09
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (11 bp):
ATGCATGTATG
Found at i:311005 original size:34 final size:36
Alignment explanation
Indices: 310965--311046 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 36
310955 AGAATATATG
310965 CATGTATGTATATATGT-ATG-ATGCATGTATGATA
1 CATGTATGTATATATGTAATGCATGCATGTATGATA
* * *
310999 CATGTATG--TGTGTGTAATGCATGCATGTATGATG
1 CATGTATGTATATATGTAATGCATGCATGTATGATA
*
311033 CATGTATATATATA
1 CATGTATGTATATA
311047 CATATATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
32 5 0.13
33 3 0.08
34 28 0.74
36 2 0.05
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.40
Consensus pattern (36 bp):
CATGTATGTATATATGTAATGCATGCATGTATGATA
Found at i:312862 original size:2 final size:2
Alignment explanation
Indices: 312855--312886 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
312845 GAACACATTA
312855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
312887 TATCAGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:328600 original size:3 final size:3
Alignment explanation
Indices: 328592--328657 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
328582 TCCGGGTCTT
328592 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
328640 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
328658 GGATAAAGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:328954 original size:35 final size:35
Alignment explanation
Indices: 328881--328966 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
328871 AAAACAGTCA
* * * *
328881 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCACAAATTCCAAAATAAT
* * * *
328916 TCAATTTTATTCTAAACCATAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCACAAATTCCAAAATAAT
*
328951 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
328967 ATACTTCAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCACAAATTCCAAAATAAT
Found at i:328960 original size:21 final size:21
Alignment explanation
Indices: 328935--328977 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
328925 TTCTAAACCA
328935 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
328956 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
328977 T
1 T
328978 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:329132 original size:16 final size:18
Alignment explanation
Indices: 329100--329133 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
329090 TATTAATGTA
329100 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
329118 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
329134 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:329806 original size:130 final size:130
Alignment explanation
Indices: 329603--329850 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
329593 AATTTTCTTC
* * * *
329603 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCATAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
329668 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
329733 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
329798 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
329851 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:330555 original size:3 final size:3
Alignment explanation
Indices: 330547--330576 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
330537 TACTTTACCC
330547 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
330577 ACAATTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:336382 original size:22 final size:23
Alignment explanation
Indices: 336341--336384 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
336331 ATGATCGAAG
**
336341 TTGGGGCAAGGGAAGCCAAATTT
1 TTGGGGCAAGGGAAAACAAATTT
336364 TTGGGGCAA-GGAAAACAAATT
1 TTGGGGCAAGGGAAAACAAATT
336385 GCATCAGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.20
Consensus pattern (23 bp):
TTGGGGCAAGGGAAAACAAATTT
Found at i:336987 original size:37 final size:36
Alignment explanation
Indices: 336924--337053 Score: 113
Period size: 37 Copynumber: 3.6 Consensus size: 36
336914 CAAAGTGTCG
* * * *
336924 TCTCTCTAGAGAAAGTTTTTGTTAAAAATAAATTTTC
1 TCTCTCTTGAGACAGTTTTT-CTAAAAACAAATTTTC
* *
336961 TCTCTCTTGAGACAGTTTTATCTAAAAACAAAATTTG
1 TCTCTCTTGAGACAGTTTT-TCTAAAAACAAATTTTC
* *
336998 TCT-TGATTGAGACAATTTTTCTAAAAACAAA-TTTC
1 TCTCT-CTTGAGACAGTTTTTCTAAAAACAAATTTTC
* *
337033 ACCTCGCTTGAGACA-TTTTTC
1 -TCTCTCTTGAGACAGTTTTTC
337054 CTTTGAGATG
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
35 9 0.12
36 23 0.30
37 44 0.57
38 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (36 bp):
TCTCTCTTGAGACAGTTTTTCTAAAAACAAATTTTC
Found at i:337044 original size:36 final size:36
Alignment explanation
Indices: 336966--337053 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 36
336956 TTTTCTCTCT
* ** *
336966 CTTGAGACAGTTTTATCTAAAAACAAAATTTGTCTTG
1 CTTGAGACAATTTT-TCTAAAAACAAAATTTACCTCG
*
337003 ATTGAGACAATTTTTCTAAAAAC-AAATTTCACCTCG
1 CTTGAGACAATTTTTCTAAAAACAAAATTT-ACCTCG
337039 CTTGAGAC-ATTTTTC
1 CTTGAGACAATTTTTC
337054 CTTTGAGATG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
35 13 0.30
36 19 0.43
37 12 0.27
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (36 bp):
CTTGAGACAATTTTTCTAAAAACAAAATTTACCTCG
Found at i:337338 original size:21 final size:21
Alignment explanation
Indices: 337309--337352 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
337299 AGCTTTTAGA
*
337309 TTGTTTCTCTTGAAACAAGTT
1 TTGTCTCTCTTGAAACAAGTT
*
337330 TTGTCTCTCTTGAAACAATTT
1 TTGTCTCTCTTGAAACAAGTT
337351 TT
1 TT
337353 TATTGAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (21 bp):
TTGTCTCTCTTGAAACAAGTT
Found at i:337448 original size:66 final size:66
Alignment explanation
Indices: 337301--337626 Score: 332
Period size: 66 Copynumber: 4.9 Consensus size: 66
337291 AATTGATAAG
* * * * * *
337301 CTTTTAGATTGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAAACAATTTTTTATTGAAACATAA
1 CTTTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGAC-AGTTTCTCTTGAAACA-AA
337366 AAC
64 AAC
* * * *
337369 CTTTAAGATTGTTTCTCTTGAAACAAGTTTTGTCTCTCTCGAGACAGTTTCTCTTGAAACACAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAA
337434 C
66 C
* * *
337435 CTTTGAGATTGTTTCCCCTGAAACAAAGTTTTTTCTCTCTTGAGACAATTTCTCTTGAAACAAAA
1 CTTTGAGATTGTTTCCCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAA
*
337500 AT
65 AC
* * * * * * *
337502 CTTTGAGATTGTTT-CCTTCAAAACAAATTTCGTCTCTCTTGAGTCATTTTCTCTTGAAACTTAT
1 CTTTGAGATTGTTTCCCTT-GAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAA
337566 AA-
64 AAC
* ** ** * * *
337568 CTTTGATACCGTTTCCCTTGAAACAAACTATGTCTCGCTTGAGATAGTTTCTCTTGAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
337627 ACATTATCCC
Statistics
Matches: 219, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
66 102 0.47
67 75 0.34
68 42 0.19
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (66 bp):
CTTTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAA
C
Found at i:337572 original size:133 final size:135
Alignment explanation
Indices: 337296--337626 Score: 368
Period size: 133 Copynumber: 2.5 Consensus size: 135
337286 AAAAAAATTG
* * * * * *
337296 ATAAGCTTTTAGATTGTTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAAACAATTTTTTATTGAA
1 ATAACCTTTGAGATTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAA-TTTCTCTTGAA
* * *
337360 ACATAAAACCTTTAAGATTGTTTCTCTTGAAACAAGTTTTGTCTCTCTCGAGACAGTTTCTCTTG
65 ACATAAAACCTTTAAGATTGTTTCTCTTAAAACAAATTTCGTCTCTCTCGAGACAGTTTCTCTTG
337425 AAACAC
130 AAACAC
* *
337431 A-AACCTTTGAGATTGTTTCCCCTGAAACAAAGTTTTTTCTCTCTTGAGACAATTTCTCTTGAAA
1 ATAACCTTTGAGATTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAA
* * * * *
337495 CA-AAAATCTTTGAGATTGTTTC-CTTCAAAACAAATTTCGTCTCTCTTGAGTCATTTTCTCTTG
66 CATAAAACCTTTAAGATTGTTTCTCTT-AAAACAAATTTCGTCTCTCTCGAGACAGTTTCTCTTG
**
337558 AAACTT
130 AAACAC
* ** * * * * *
337564 ATAA-CTTTGATACCGTTTCCCTTGAAACAAA-CTATGTCTCGCTTGAGATAGTTTCTCTTGAAA
1 ATAACCTTTGAGATTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAA
337627 ACATTATCCC
Statistics
Matches: 165, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
132 29 0.18
133 77 0.47
134 37 0.22
135 22 0.13
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (135 bp):
ATAACCTTTGAGATTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAA
CATAAAACCTTTAAGATTGTTTCTCTTAAAACAAATTTCGTCTCTCTCGAGACAGTTTCTCTTGA
AACAC
Found at i:337849 original size:54 final size:55
Alignment explanation
Indices: 337736--337866 Score: 176
Period size: 54 Copynumber: 2.4 Consensus size: 55
337726 TAGCCAAACT
* *
337736 TCCTCATCATGTAGGAACCGCATTATCTTTATTATCCCTAAAGATGGCCAGCCAG
1 TCCTCATCATGTAGGAACCGTATTATCTTCATTATCCCTAAAGATGGCCAGCCAG
* ** *
337791 -CCTCATCATGTAGGAACCGTGTTATCTTCATTATCCCTAAAGATTTCCAGTC-G
1 TCCTCATCATGTAGGAACCGTATTATCTTCATTATCCCTAAAGATGGCCAGCCAG
* *
337844 TCCTCATCACGTAAGAACCGTAT
1 TCCTCATCATGTAGGAACCGTAT
337867 CATCCACCGA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
53 1 0.02
54 65 0.98
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (55 bp):
TCCTCATCATGTAGGAACCGTATTATCTTCATTATCCCTAAAGATGGCCAGCCAG
Found at i:337963 original size:191 final size:191
Alignment explanation
Indices: 337653--338003 Score: 531
Period size: 191 Copynumber: 1.8 Consensus size: 191
337643 TGGCCAACCA
* * * *
337653 TCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCTCCTCATCACGTAAGAGCTACGTCA
1 TCCTCATCACGTAAGAACCGTATCATCCACCGACCAGATCTCCTCATCACGTAAGAGCCACGTCA
* * **
337718 CCCTTAGATAGCCAAACTTCCTCATCATGTAGGAACCGCATTATCTTTATTATCCCTAAAGATGG
66 CCCTTAGATAGCCAAACTTCCTCATCACGTAGGAACCACATTATCTAAATTATCCCTAAAGATGG
337783 CCAGCCAGCCTCATCATGTAGGAACCGTGTTATCTTCATTATCCCTAAAGATTTCCAGTCG
131 CCAGCCAGCCTCATCATGTAGGAACCGTGTTATCTTCATTATCCCTAAAGATTTCCAGTCG
* * *
337844 TCCTCATCACGTAAGAACCGTATCATCCACCGATCAGATCTCCTCATCACGTAGGAGCCGCGTCA
1 TCCTCATCACGTAAGAACCGTATCATCCACCGACCAGATCTCCTCATCACGTAAGAGCCACGTCA
* * ** *
337909 CCCTTAGGTAGCCAGACTTCCTCATCACGTAGGAACCATGTTATCTAAATTATCCTTAAAGATGG
66 CCCTTAGATAGCCAAACTTCCTCATCACGTAGGAACCACATTATCTAAATTATCCCTAAAGATGG
* * *
337974 CTAGTCATCCTCATCATGTAGGAACCGTGT
131 CCAGCCAGCCTCATCATGTAGGAACCGTGT
338004 CATCCACCGA
Statistics
Matches: 141, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
191 141 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (191 bp):
TCCTCATCACGTAAGAACCGTATCATCCACCGACCAGATCTCCTCATCACGTAAGAGCCACGTCA
CCCTTAGATAGCCAAACTTCCTCATCACGTAGGAACCACATTATCTAAATTATCCCTAAAGATGG
CCAGCCAGCCTCATCATGTAGGAACCGTGTTATCTTCATTATCCCTAAAGATTTCCAGTCG
Found at i:338028 original size:137 final size:137
Alignment explanation
Indices: 337791--338224 Score: 582
Period size: 137 Copynumber: 3.2 Consensus size: 137
337781 GGCCAGCCAG
* * ** * *
337791 CCTCATCATGTAGGAACCGTGTTATCTTCATTATCCCTAAAGATTTCCAGTCGTCCTCATCACGT
1 CCTCATCACGTAGGAACCGTGTTATCTACATTATCCCTAAAGATGGCTAGTCATCCTCATCACGT
* * * *
337856 AAGAACCGTATCATCCACCGATCAGATCTCCTCATCACGTAGGAGCCGCGTCACCCTTAGGTAGC
66 AGGAACCGTGTCATCCACCGATCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATAGC
337921 CAGACTT
131 CAGACTT
* * * *
337928 CCTCATCACGTAGGAACCATGTTATCTAAATTATCCTTAAAGATGGCTAGTCATCCTCATCATGT
1 CCTCATCACGTAGGAACCGTGTTATCTACATTATCCCTAAAGATGGCTAGTCATCCTCATCACGT
* * *
337993 AGGAACCGTGTCATCCACCGATCATATCTCCTCATCACATATGAGCCGTGTCACCCTTAGATAGC
66 AGGAACCGTGTCATCCACCGATCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATAGC
338058 CAGACTT
131 CAGACTT
* * * * **
338065 CCTCATCGCGTAAGAATCGTGTTATCTACATTATCCCTAAAGACGG-TCAACCATCCTCATCACG
1 CCTCATCACGTAGGAACCGTGTTATCTACATTATCCCTAAAGATGGCT-AGTCATCCTCATCACG
* * * *
338129 TAGGAACTGTGTCATCCACCGACCAGATCTCCTCATCATGTAGGAGCCATGTCACCCTTAGATAG
65 TAGGAACCGTGTCATCCACCGATCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATAG
338194 CCAGACTT
130 CCAGACTT
* * *
338202 CCTCATCACATATGAATCGTGTT
1 CCTCATCACGTAGGAACCGTGTT
338225 CTCCAAATTT
Statistics
Matches: 259, Mismatches: 37, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
136 1 0.00
137 258 1.00
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (137 bp):
CCTCATCACGTAGGAACCGTGTTATCTACATTATCCCTAAAGATGGCTAGTCATCCTCATCACGT
AGGAACCGTGTCATCCACCGATCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATAGC
CAGACTT
Found at i:338446 original size:3 final size:3
Alignment explanation
Indices: 338440--338474 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
338430 ATTATTATTA
338440 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
338475 AATTTACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:344974 original size:22 final size:22
Alignment explanation
Indices: 344946--345002 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
344936 GGGAGCGTAT
344946 GGGTATTGGTACTCCTTCATAG
1 GGGTATTGGTACTCCTTCATAG
344968 GGGTATTGGTACTCCTTCATAG
1 GGGTATTGGTACTCCTTCATAG
*
344990 GGGTATCGGTACT
1 GGGTATTGGTACT
345003 ACCTGTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.35
Consensus pattern (22 bp):
GGGTATTGGTACTCCTTCATAG
Found at i:345100 original size:6 final size:6
Alignment explanation
Indices: 345089--345147 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
345079 TATGTAAGGT
* * * *
345089 GGTATC GGTATC GATACC GGTCAT- GGTATC GGTATC GATACC GGTCAT-
1 GGTATC GGTATC GGTATC GGT-ATC GGTATC GGTATC GGTATC GGT-ATC
345137 GGTATC GGTAT
1 GGTATC GGTAT
345148 TGATACCAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
5 4 0.10
6 35 0.85
7 2 0.05
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.31
Consensus pattern (6 bp):
GGTATC
Found at i:345115 original size:24 final size:24
Alignment explanation
Indices: 345088--345170 Score: 148
Period size: 24 Copynumber: 3.5 Consensus size: 24
345078 CTATGTAAGG
345088 TGGTATCGGTATCGATACCGGTCA
1 TGGTATCGGTATCGATACCGGTCA
345112 TGGTATCGGTATCGATACCGGTCA
1 TGGTATCGGTATCGATACCGGTCA
* *
345136 TGGTATCGGTATTGATACCAGTCA
1 TGGTATCGGTATCGATACCGGTCA
345160 TGGTATCGGTA
1 TGGTATCGGTA
345171 CCTATTTTGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (24 bp):
TGGTATCGGTATCGATACCGGTCA
Found at i:350164 original size:174 final size:174
Alignment explanation
Indices: 349874--350222 Score: 689
Period size: 174 Copynumber: 2.0 Consensus size: 174
349864 AGATCACCTA
349874 CAATCTCACCATCCTTGATATAGTTGTATTCTCTTGGGTATGTGATTTCCCTTTCTTCAATGGTT
1 CAATCTCACCATCCTTGATATAGTTGTATTCTCTTGGGTATGTGATTTCCCTTTCTTCAATGGTT
*
349939 CGATTCTTTAAGGAATCTTCAGTTTCCCCATCCTTCACTTCTTCCTTTGATGATGATTCTCCCAC
66 AGATTCTTTAAGGAATCTTCAGTTTCCCCATCCTTCACTTCTTCCTTTGATGATGATTCTCCCAC
350004 GTCATTTGCATTTATTATACCTACGTCATCATCAACACAAGAAT
131 GTCATTTGCATTTATTATACCTACGTCATCATCAACACAAGAAT
350048 CAATCTCACCATCCTTGATATAGTTGTATTCTCTTGGGTATGTGATTTCCCTTTCTTCAATGGTT
1 CAATCTCACCATCCTTGATATAGTTGTATTCTCTTGGGTATGTGATTTCCCTTTCTTCAATGGTT
350113 AGATTCTTTAAGGAATCTTCAGTTTCCCCATCCTTCACTTCTTCCTTTGATGATGATTCTCCCAC
66 AGATTCTTTAAGGAATCTTCAGTTTCCCCATCCTTCACTTCTTCCTTTGATGATGATTCTCCCAC
350178 GTCATTTGCATTTATTATACCTACGTCATCATCAACACAAGAAT
131 GTCATTTGCATTTATTATACCTACGTCATCATCAACACAAGAAT
350222 C
1 C
350223 CTTCCTCAGA
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (174 bp):
CAATCTCACCATCCTTGATATAGTTGTATTCTCTTGGGTATGTGATTTCCCTTTCTTCAATGGTT
AGATTCTTTAAGGAATCTTCAGTTTCCCCATCCTTCACTTCTTCCTTTGATGATGATTCTCCCAC
GTCATTTGCATTTATTATACCTACGTCATCATCAACACAAGAAT
Found at i:371977 original size:14 final size:14
Alignment explanation
Indices: 371950--371986 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
371940 AACCCATGTT
* *
371950 TCTTCTTATGCTTC
1 TCTTCGTATACTTC
371964 TCTTCGTATACTTC
1 TCTTCGTATACTTC
371978 TCTTCGTAT
1 TCTTCGTAT
371987 GCTTGCAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.27, G:0.08, T:0.54
Consensus pattern (14 bp):
TCTTCGTATACTTC
Found at i:381739 original size:17 final size:17
Alignment explanation
Indices: 381713--381762 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 17
381703 AGAAAAAAAA
* *
381713 TATTATTTTAAAGAGGT
1 TATTAATTTATAGAGGT
*
381730 TATTAATTTATTGA-G-
1 TATTAATTTATAGAGGT
381745 TATTAATTTATAGAGGT
1 TATTAATTTATAGAGGT
381762 T
1 T
381763 CTACTGTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 13 0.48
16 2 0.07
17 12 0.44
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (17 bp):
TATTAATTTATAGAGGT
Found at i:382517 original size:31 final size:32
Alignment explanation
Indices: 382464--382525 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
382454 TACAGTCTCC
* * *
382464 CAACATTTAGTTCATTTTCAATATGG-CCCCT
1 CAACATTTAGTCCACTTGCAATATGGACCCCT
*
382495 CAACATTTAGTCCGCTTGCAATATGGACCCC
1 CAACATTTAGTCCACTTGCAATATGGACCCC
382526 GACGTAATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (32 bp):
CAACATTTAGTCCACTTGCAATATGGACCCCT
Found at i:384709 original size:36 final size:35
Alignment explanation
Indices: 384667--384801 Score: 207
Period size: 36 Copynumber: 3.8 Consensus size: 35
384657 GTGCGATACA
* *
384667 TCTTCCGTTCGATTAGAATCGGAAGTGCCGATGCT
1 TCTTCCGTTCGATTTGAATCGGAAGTGCCGATGCC
384702 TCCTTCCGTTCGATTTGAATCGGAAGTGCCGATGCC
1 T-CTTCCGTTCGATTTGAATCGGAAGTGCCGATGCC
* *
384738 TACTTCCATTCAATTTGAATCGGAAGTGCCGATGCC
1 T-CTTCCGTTCGATTTGAATCGGAAGTGCCGATGCC
*
384774 TCTTCCGTTCTATTTGAATCGGAAGTGC
1 TCTTCCGTTCGATTTGAATCGGAAGTGC
384802 ATGCTTTCTT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 26 0.28
36 66 0.72
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (35 bp):
TCTTCCGTTCGATTTGAATCGGAAGTGCCGATGCC
Found at i:394259 original size:85 final size:85
Alignment explanation
Indices: 394125--394297 Score: 206
Period size: 85 Copynumber: 2.0 Consensus size: 85
394115 GCAATTGTAC
* * ** * *
394125 GTCATAAATTTATGACGCGCATTTATGACGCTCATTGCGCGTCTTTGAAGCCCCCGTCA-TAAAT
1 GTCATAAATTTATGACACGCATTTATGACGCTCATTACGCGTCACTGAAGCACACGTCATTAAA-
*
394189 AAAGACGACACACATTTGTGT
65 AAAGACGACACACATTCGTGT
* * * *
394210 GTCATAAATTTATGACATGCATTTATGAC-TTACATTACGTGTCACTGAAGCACACGTCATTAGA
1 GTCATAAATTTATGACACGCATTTATGACGCT-CATTACGCGTCACTGAAGCACACGTCATTAAA
*
394274 AAAGATGACACACATTCGTGT
65 AAAGACGACACACATTCGTGT
394295 GTC
1 GTC
394298 GTGATTGTAT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
84 1 0.01
85 70 0.95
86 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (85 bp):
GTCATAAATTTATGACACGCATTTATGACGCTCATTACGCGTCACTGAAGCACACGTCATTAAAA
AAGACGACACACATTCGTGT
Found at i:394324 original size:2 final size:2
Alignment explanation
Indices: 394317--394353 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
394307 TGTCGTAAAT
394317 TA TA TA 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 TA TA TA T
394354 TGTAGATTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:398502 original size:9 final size:9
Alignment explanation
Indices: 398488--398512 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
398478 CTTAAAGTAT
398488 GAAATGTTA
1 GAAATGTTA
398497 GAAATGTTA
1 GAAATGTTA
398506 GAAATGT
1 GAAATGT
398513 GAATGGACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (9 bp):
GAAATGTTA
Found at i:415439 original size:20 final size:21
Alignment explanation
Indices: 415414--415467 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
415404 TTTGGTTCAC
*
415414 GGAATATAAGATTAAT-AGTG
1 GGAATAAAAGATTAATCAGTG
415434 GGAATAAAAGATT-ATCAGTG
1 GGAATAAAAGATTAATCAGTG
*
415454 TGAATAAAAGATTA
1 GGAATAAAAGATTA
415468 CCAGATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.48, C:0.02, G:0.22, T:0.28
Consensus pattern (21 bp):
GGAATAAAAGATTAATCAGTG
Found at i:430158 original size:42 final size:42
Alignment explanation
Indices: 430099--430216 Score: 200
Period size: 42 Copynumber: 2.8 Consensus size: 42
430089 CATCTTCTAC
* *
430099 TTTGTCAACATATATGCTCCTTGCGATGTTTTTTCCGTGACA
1 TTTGTCAATATATATGCTCCTTGCGATGTTTTTGCCGTGACA
* *
430141 TTTGTCAATATATATGCTCCTTGTGATGTTTTTGCCGTGACC
1 TTTGTCAATATATATGCTCCTTGCGATGTTTTTGCCGTGACA
430183 TTTGTCAATATATATGCTCCTTGCGATGTTTTTG
1 TTTGTCAATATATATGCTCCTTGCGATGTTTTTG
430217 TCTTAACCTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTGTCAATATATATGCTCCTTGCGATGTTTTTGCCGTGACA
Found at i:430226 original size:42 final size:42
Alignment explanation
Indices: 430098--430229 Score: 194
Period size: 42 Copynumber: 3.1 Consensus size: 42
430088 TCATCTTCTA
*
430098 CTTTGTCAACATATATGCTCCTTGCGATGTTTTT-TCCGTGAC
1 CTTTGTCAATATATATGCTCCTTGCGATGTTTTTGT-CGTGAC
* * *
430140 ATTTGTCAATATATATGCTCCTTGTGATGTTTTTGCCGTGAC
1 CTTTGTCAATATATATGCTCCTTGCGATGTTTTTGTCGTGAC
* *
430182 CTTTGTCAATATATATGCTCCTTGCGATGTTTTTGTCTTAAC
1 CTTTGTCAATATATATGCTCCTTGCGATGTTTTTGTCGTGAC
430224 CTTTGT
1 CTTTGT
430230 GTCAACTGTA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (42 bp):
CTTTGTCAATATATATGCTCCTTGCGATGTTTTTGTCGTGAC
Found at i:430889 original size:3 final size:3
Alignment explanation
Indices: 430881--430906 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
430871 TAAAAAATCA
430881 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
430907 ATGATACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:435368 original size:39 final size:39
Alignment explanation
Indices: 435317--435399 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
435307 CTCATGATTT
435317 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
* *
435356 TATCAAAGCCATGATAAACAATATTATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
435395 TATCA
1 TATCA
435400 TATTCTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (39 bp):
TATCAAAACCATGATAAACAATATCATACATAATAGTCA
Found at i:435449 original size:13 final size:13
Alignment explanation
Indices: 435429--435473 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
435419 ACAATACAAA
435429 ACTTTCATATCTC
1 ACTTTCATATCTC
*
435442 ATTTTCATCAT-TC
1 ACTTTCAT-ATCTC
435455 ACTTTCATA-CTC
1 ACTTTCATATCTC
435467 ACTTTCA
1 ACTTTCA
435474 CATTTTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 10 0.36
13 16 0.57
14 2 0.07
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (13 bp):
ACTTTCATATCTC
Found at i:435458 original size:26 final size:24
Alignment explanation
Indices: 435429--435477 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
435419 ACAATACAAA
*
435429 ACTTTCATATCTCATTTTCATCATTC
1 ACTTTCATA-CTCACTTTCA-CATTC
435455 ACTTTCATACTCACTTTCACATT
1 ACTTTCATACTCACTTTCACATT
435478 TTGTTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.18
25 9 0.41
26 9 0.41
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (24 bp):
ACTTTCATACTCACTTTCACATTC
Done.