Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007733.1 Hibiscus syriacus cultivar Beakdansim tig00109987_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: 1979160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:1096931 original size:15 final size:15
Alignment explanation
Indices: 1096911--1096939 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1096901 TATGTGTGTG
1096911 TATATATATATATAT
1 TATATATATATATAT
1096926 TATATATATATATA
1 TATATATATATATA
1096940 AAGTTCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:1097612 original size:12 final size:12
Alignment explanation
Indices: 1097595--1097621 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1097585 CCATTGCAAT
1097595 TATGTGTGTGTA
1 TATGTGTGTGTA
1097607 TATGTGTGTGTA
1 TATGTGTGTGTA
1097619 TAT
1 TAT
1097622 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.52
Consensus pattern (12 bp):
TATGTGTGTGTA
Found at i:1100104 original size:31 final size:32
Alignment explanation
Indices: 1100051--1100114 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
1100041 ATTAGATGTG
1100051 AAAGGCCAACGAAAATTGAACCAAATGTTGGT
1 AAAGGCCAACGAAAATTGAACCAAATGTTGGT
**
1100083 AAAGGCCAACG-AGTTTGAACCAAATGTTGGT
1 AAAGGCCAACGAAAATTGAACCAAATGTTGGT
1100114 A
1 A
1100115 TTTTTAGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (32 bp):
AAAGGCCAACGAAAATTGAACCAAATGTTGGT
Found at i:1103906 original size:235 final size:235
Alignment explanation
Indices: 1103137--1104979 Score: 2346
Period size: 235 Copynumber: 7.9 Consensus size: 235
1103127 CTGAAAATCG
* * *
1103137 ATAATTGTAGTTCATATTTGTGGTC--TG-TGTT---ATTCGG-TATAAGTGTCGGGTATTTATT
1 ATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGGATATAAGTGTCAGGTATATATT
* * **
1103195 AGACATGGTATAATTAGAATTTTCAAGGTTTTTCCATGTACTTAAAGGATCTTTGCGGTTCATAT
66 AGACATGTTATAATTAGAATTTTCAAAGTTTTTCCATGTACTTTGAGGATCTTTGCGGTTCATAT
* * * *
1103260 TCATGTGTCCGACACAGCTATCGGAGTCTAAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACA
131 CCATGTGTCGGACACTGCTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACA
* *
1103325 GTCCAATATCTGAGTTTTGGTATTTACAGCAATCACTCCA
196 GTCCAATATCTGAGTTTTGGTATTTACAGCTATCAGTCCA
* * * * *
1103365 ATAATTGTAGTTCATGTTTGTGGTATTTGTTATTCAGATTCGAATATAAGTGTCACAGGTATACA
1 ATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGGATATAAGTGT--CAGGTATATA
* ** * *
1103430 TTAGACATGTTGTAATTAGAATTTTTGAAGTTTTTTCATGTAC-TT--GGA-CTTGGAGTGCAGT
64 TTAGACATGTTATAATTAGAATTTTCAAAGTTTTTCCATGTACTTTGAGGATCTT----TGCGGT
* * ** * *
1103491 TCATATCCATGTCTTGGACACAACTATCAGAGTCTTGAGGCTCTGAGCAACATAGCTTGTGGCTA
125 TCATATCCATGTGTCGGACACTGCTATC---G----GA-G-TCTGAGCAGCATAGTTTGTGGCTA
* *
1103556 CTTGTGGTGTTTCCAGTCCAATATTTGAGTTTTGGTATTTACAGCTATCAAGTCCA
181 CTTGTGGTGTTTACAGTCCAATATCTGAGTTTTGGTATTTACAGCTATC-AGTCCA
* *
1103612 ATAATTGTAGTTCAGATTTGTGGTCTTTGTTACTCGGATTCGGATATAAGTGTCAGGTATATATT
1 ATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGGATATAAGTGTCAGGTATATATT
*
1103677 CA-ACATGTTATAATTAGAATTTTCAAAGTTTTTCCATGTACTTTGAGGATTTTTGCGGTTCATA
66 -AGACATGTTATAATTAGAATTTTCAAAGTTTTTCCATGTACTTTGAGGATCTTTGCGGTTCATA
* * * * *
1103741 TCCATGTGTCGGGCACTGTTATCGTAGTCTGAGGAGCATAGTTTGTGGCTACTTGTGTTGTTTAC
130 TCCATGTGTCGGACACTGCTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTAC
*
1103806 AGTCCAATATCTGAGTTTTTGTATTTACAGCTATCAGTCCA
195 AGTCCAATATCTGAGTTTTGGTATTTACAGCTATCAGTCCA
* * *
1103847 ATATTTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGAATATAAGTGCCAGGTATATATT
1 ATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGGATATAAGTGTCAGGTATATATT
* * * *
1103912 AGAC--------A-T-G--TTTTCTAAGATTTTACATGTACTTTGAGGATCTTTGTGGTTCATAT
66 AGACATGTTATAATTAGAATTTTCAAAGTTTTTCCATGTACTTTGAGGATCTTTGCGGTTCATAT
*
1103965 CCATGTGTCCGACA-TGACTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTAC
131 CCATGTGTCGGACACTG-CTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTAC
1104029 AGTCCAATATCTGAGTTTTGGTATTTACAGCTATCAGTCCA
195 AGTCCAATATCTGAGTTTTGGTATTTACAGCTATCAGTCCA
*
1104070 ATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGAATA-AAGTGTCAGGTATATATT
1 ATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGGATATAAGTGTCAGGTATATATT
* *
1104134 AGACATGTTATGATTAGAATTTTCAAAGTTTTT--ATGTACTTTGAGGATCTTTGCAGTTCATAT
66 AGACATGTTATAATTAGAATTTTCAAAGTTTTTCCATGTACTTTGAGGATCTTTGCGGTTCATAT
* * *
1104197 CCATGTGCCAGACAATGCTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACA
131 CCATGTGTCGGACACTGCTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACA
* * *
1104262 GTTCAATACCTGAGTTTTGGTATTTACAACTATCAGTCCA
196 GTCCAATATCTGAGTTTTGGTATTTACAGCTATCAGTCCA
* *
1104302 ATAATTGTAGTTCATATTTGTGGTCTTTGTTTTTCGGATTCGGATATAAGAGTCAGGTATATATT
1 ATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGGATATAAGTGTCAGGTATATATT
* * *
1104367 AGGA-ATGTTATAATTAGAATCTTCAAAGTTTTTCCATGTACTTTGAGGATTTTTGCAGTTCATA
66 A-GACATGTTATAATTAGAATTTTCAAAGTTTTTCCATGTACTTTGAGGATCTTTGCGGTTCATA
* * *
1104431 TCCATGTGTCGGGCACTGTTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGTTGTTTAC
130 TCCATGTGTCGGACACTGCTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTAC
* *
1104496 AGTCCAATATCTGAGTTTTTGTATTTACAGCTATCAATCCA
195 AGTCCAATATCTGAGTTTTGGTATTTACAGCTATCAGTCCA
* * * *
1104537 ATAATTGCAGTTCATATTTGTTGTCTTTGTTATTCGGATTCGGATATAAGTGTGAGGTATATGTT
1 ATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGGATATAAGTGTCAGGTATATATT
* *
1104602 AGACATGTTATAAGTAGAATTTTCAAA-TTTCTTTCATGTACTTTGAGGATCTTTGCGGTTCATA
66 AGACATGTTATAATTAGAATTTTCAAAGTTT-TTCCATGTACTTTGAGGATCTTTGCGGTTCATA
* * **
1104666 -CTCATGTGTCTGACGCTGCTATCGGAGTCTGAGCAAGCATAGTTTGTGGCTACTTGCAGTGTTT
130 TC-CATGTGTCGGACACTGCTATCGGAGTCTGAGC-AGCATAGTTTGTGGCTACTTGTGGTGTTT
* *
1104730 TCAGTCCAATATATGAGTTTTGGTA-TT-----TA-CAGTCCA
193 ACAGTCCAATATCTGAGTTTTGGTATTTACAGCTATCAGTCCA
* * *
1104766 ATAATTGTAGTTCATATTTGTGATCTTTGTTTTTCGGATTCGGATATAAGT-T--GGTATATTTT
1 ATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGGATATAAGTGTCAGGTATATATT
* ** * *
1104828 AGACATGTTATAATCAGAATTTTCAAAGTTTTTCCATGTACTTAAAGGATTTTTGTGGTTCATAT
66 AGACATGTTATAATTAGAATTTTCAAAGTTTTTCCATGTACTTTGAGGATCTTTGCGGTTCATAT
* ** * * * *
1104893 CCATGTCTCGGACACAACTATCGGAGTCTGAGCAACATAGTTTGCGGATACTTGTGGTGTTTGCA
131 CCATGTGTCGGACACTGCTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACA
*
1104958 GTCTAATATCTGAGTTTTGGTA
196 GTCCAATATCTGAGTTTTGGTA
1104980 GTGATGACTG
Statistics
Matches: 1416, Mismatches: 146, Indels: 109
0.85 0.09 0.07
Matches are distributed among these distances:
222 23 0.02
223 181 0.13
225 47 0.03
226 90 0.06
227 5 0.00
228 24 0.02
229 53 0.04
230 5 0.00
231 4 0.00
232 170 0.12
233 50 0.04
234 29 0.02
235 341 0.24
236 115 0.08
237 73 0.05
238 1 0.00
240 1 0.00
242 1 0.00
244 2 0.00
245 74 0.05
246 70 0.05
247 52 0.04
248 3 0.00
249 2 0.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (235 bp):
ATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGGATATAAGTGTCAGGTATATATT
AGACATGTTATAATTAGAATTTTCAAAGTTTTTCCATGTACTTTGAGGATCTTTGCGGTTCATAT
CCATGTGTCGGACACTGCTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACA
GTCCAATATCTGAGTTTTGGTATTTACAGCTATCAGTCCA
Found at i:1104565 original size:690 final size:696
Alignment explanation
Indices: 1103223--1104979 Score: 2368
Period size: 690 Copynumber: 2.5 Consensus size: 696
1103213 ATTTTCAAGG
* ** * *
1103223 TTTTTCCATGTACTTAAAGGATCTTTGCGGTTCATATTCATGTGTCCGACA-CAGCTATCGGAGT
1 TTTTTACATGTACTTTGAGGATCTTTGCGGTTCATATCCATGTGTCCGACATGA-CTATCGGAGT
*
1103287 CTAAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACAGTCCAATATCTGAGTTTTGGTATTTAC
65 CTGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACAGTCCAATATCTGAGTTTTGGTATTTAC
* * * * *
1103352 AGCAATCACTCCAATAATTGTAGTTCATGTTTGTGGTATTTGTTATTCAGATTCGAATATAAGTG
130 AGCTATCAGTCCAATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGAATATAAGTG
* * **
1103417 TCACAGGTATACATTAGACATGTTGTAATTAGAATTTTTGAAGTTTTTTCATGTAC-TT-GGA-C
195 T--CAGGTATATATTAGACATGTTATAATTAGAATTTTCAAAG-TTTTTCATGTACTTTAGGATC
* * *
1103479 TTGGAGTGCAGTTCATATCCATGTCTTGGACACA-ACTATCAGAGTCTTGAGGCTCTGAGCAACA
257 TT----TGCAGTTCATATCCATG---T-G-CACAGACAATC-TA-TC-GGA-G-TCTGAGCAACA
* * * * *
1103543 TAGCTTGTGGCTACTTGTGGTGTTTCCAGTCCAATATTTGAGTTTTGGTATTTACAGCTATCAAG
308 TAGTTTGTGGCTACTTGTGGTGTTTACAGTTCAATATCTGAGTTTTGGTATTTACAACTATCAAG
*
1103608 TCCAATAATTGTAGTTCAGATTTGTGGTCTTTGTTACTCGGATTCGGATATAAGTGTCAGGTATA
373 TCCAATAATTGTAGTTCAGATTTGTGGTCTTTGTTACTCGGATTCGGATATAAGAGTCAGGTATA
* *
1103673 TATTCAACATGTTATAATTAGAATTTTCAAAGTTTTTCCATGTACTTTGAGGATTTTTGCGGTTC
438 TATTCAACATGTTATAATTAGAATCTTCAAAGTTTTTCCATGTACTTTGAGGATTTTTGCAGTTC
* *
1103738 ATATCCATGTGTCGGGCACTGTTATCGTAGTCTGAGGAGCATAGTTTGTGGCTACTTGTGTTGTT
503 ATATCCATGTGTCGGGCACTGTTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGTTGTT
* * *
1103803 TACAGTCCAATATCTGAGTTTTTGTATTTACAGCTATCAGTCCAATATTTGTAGTTCATATTTGT
568 TACAGTCCAATATCTGAGTTTTTGTATTTACAGCTATCAATCCAATAATTGCAGTTCATATTTGT
1103868 GGTCTTTGTTATTCGGATTCGAATATAAGTGCCAGGTATATATTAGACATG-T-T-TTCT-AAGA
633 GGTCTTTGTTATTCGGATTCGAATATAAGTGCCAGGTATATATTAGACATGTTATATTCTCAA-A
*
1103929 -TTTTACATGTACTTTGAGGATCTTTGTGGTTCATATCCATGTGTCCGACATGACTATCGGAGTC
1 TTTTTACATGTACTTTGAGGATCTTTGCGGTTCATATCCATGTGTCCGACATGACTATCGGAGTC
1103993 TGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACAGTCCAATATCTGAGTTTTGGTATTTACA
66 TGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACAGTCCAATATCTGAGTTTTGGTATTTACA
1104058 GCTATCAGTCCAATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGAATA-AAGTGT
131 GCTATCAGTCCAATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGAATATAAGTGT
*
1104122 CAGGTATATATTAGACATGTTATGATTAGAATTTTCAAAGTTTTT-ATGTACTTTGAGGATCTTT
196 CAGGTATATATTAGACATGTTATAATTAGAATTTTCAAAGTTTTTCATGTACTTT-AGGATCTTT
*
1104186 GCAGTTCATATCCATGTGC-CAGACAATGCTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTT
260 GCAGTTCATATCCATGTGCACAGACAAT-CTATCGGAGTCTGAGCAACATAGTTTGTGGCTACTT
*
1104250 GTGGTGTTTACAGTTCAATACCTGAGTTTTGGTATTTACAACTATC-AGTCCAATAATTGTAGTT
324 GTGGTGTTTACAGTTCAATATCTGAGTTTTGGTATTTACAACTATCAAGTCCAATAATTGTAGTT
* **
1104314 CATATTTGTGGTCTTTGTTTTTCGGATTCGGATATAAGAGTCAGGTATATATT-AGGA-ATGTTA
389 CAGATTTGTGGTCTTTGTTACTCGGATTCGGATATAAGAGTCAGGTATATATTCA--ACATGTTA
1104377 TAATTAGAATCTTCAAAGTTTTTCCATGTACTTTGAGGATTTTTGCAGTTCATATCCATGTGTCG
452 TAATTAGAATCTTCAAAGTTTTTCCATGTACTTTGAGGATTTTTGCAGTTCATATCCATGTGTCG
1104442 GGCACTGTTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGTTGTTTACAGTCCAATATC
517 GGCACTGTTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGTTGTTTACAGTCCAATATC
*
1104507 TGAGTTTTTGTATTTACAGCTATCAATCCAATAATTGCAGTTCATATTTGTTGTCTTTGTTATTC
582 TGAGTTTTTGTATTTACAGCTATCAATCCAATAATTGCAGTTCATATTTGTGGTCTTTGTTATTC
* ** * *
1104572 GGATTCGGATATAAGTGTGAGGTATATGTTAGACATGTTATAAGTAGAATTTTCAAA
647 GGATTCGAATATAAGTGCCAGGTATATATTAGACATG-T-T-A-T---ATTCTCAAA
* * *
1104629 TTTCTTTCATGTACTTTGAGGATCTTTGCGGTTCATA-CTCATGTGTCTGACGCTG-CTATCGGA
1 TTT-TTACATGTACTTTGAGGATCTTTGCGGTTCATATC-CATGTGTCCGAC-ATGACTATCGGA
** * *
1104692 GTCTGAGCAAGCATAGTTTGTGGCTACTTGCAGTGTTTTCAGTCCAATATATGAGTTTTGGTA-T
63 GTCTGAGC-AGCATAGTTTGTGGCTACTTGTGGTGTTTACAGTCCAATATCTGAGTTTTGGTATT
* * *
1104756 T-----TA-CAGTCCAATAATTGTAGTTCATATTTGTGATCTTTGTTTTTCGGATTCGGATATAA
127 TACAGCTATCAGTCCAATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGAATATAA
* * *
1104815 GT-T--GGTATATTTTAGACATGTTATAATCAGAATTTTCAAAGTTTTTCCATGTACTTAAAGGA
192 GTGTCAGGTATATATTAGACATGTTATAATTAGAATTTTCAAAGTTTTT-CATGTACTT-TAGGA
* ** * * * * *
1104877 TTTTTGTGGTTCATATCCATGT-CTCGGACACAACTATCGGAGTCTGAGCAACATAGTTTGCGGA
255 TCTTTGCAGTTCATATCCATGTGCACAGACA-ATCTATCGGAGTCTGAGCAACATAGTTTGTGGC
*
1104941 TACTTGTGGTGTTTGCAG-TCTAATATCTGAGTTTTGGTA
319 TACTTGTGGTGTTTACAGTTC-AATATCTGAGTTTTGGTA
1104980 GTGATGACTG
Statistics
Matches: 950, Mismatches: 69, Indels: 74
0.87 0.06 0.07
Matches are distributed among these distances:
689 1 0.00
690 293 0.31
691 67 0.07
692 1 0.00
693 3 0.00
694 44 0.05
695 9 0.01
696 152 0.16
697 8 0.01
700 27 0.03
701 12 0.01
702 95 0.10
703 55 0.06
704 9 0.01
705 173 0.18
706 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (696 bp):
TTTTTACATGTACTTTGAGGATCTTTGCGGTTCATATCCATGTGTCCGACATGACTATCGGAGTC
TGAGCAGCATAGTTTGTGGCTACTTGTGGTGTTTACAGTCCAATATCTGAGTTTTGGTATTTACA
GCTATCAGTCCAATAATTGTAGTTCATATTTGTGGTCTTTGTTATTCGGATTCGAATATAAGTGT
CAGGTATATATTAGACATGTTATAATTAGAATTTTCAAAGTTTTTCATGTACTTTAGGATCTTTG
CAGTTCATATCCATGTGCACAGACAATCTATCGGAGTCTGAGCAACATAGTTTGTGGCTACTTGT
GGTGTTTACAGTTCAATATCTGAGTTTTGGTATTTACAACTATCAAGTCCAATAATTGTAGTTCA
GATTTGTGGTCTTTGTTACTCGGATTCGGATATAAGAGTCAGGTATATATTCAACATGTTATAAT
TAGAATCTTCAAAGTTTTTCCATGTACTTTGAGGATTTTTGCAGTTCATATCCATGTGTCGGGCA
CTGTTATCGGAGTCTGAGCAGCATAGTTTGTGGCTACTTGTGTTGTTTACAGTCCAATATCTGAG
TTTTTGTATTTACAGCTATCAATCCAATAATTGCAGTTCATATTTGTGGTCTTTGTTATTCGGAT
TCGAATATAAGTGCCAGGTATATATTAGACATGTTATATTCTCAAA
Found at i:1106042 original size:63 final size:63
Alignment explanation
Indices: 1105943--1106068 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
1105933 ATTCCGATCG
* *
1105943 AAATGATTCTGAAGAAAAATCGAGATGTGGTTCAAATCCTAATGGGATATCAGAAAACTCTTC
1 AAATGATTCTGAAGAAAAATCGAGATGTGGTACAAATCCTAATGGGACATCAGAAAACTCTTC
*
1106006 AAATGATTCTGAAGATAAATCGAGATGTGGTACAAATCCTAATGGGACATCAGAAAACTCTTC
1 AAATGATTCTGAAGAAAAATCGAGATGTGGTACAAATCCTAATGGGACATCAGAAAACTCTTC
1106069 GACAGAGCCG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (63 bp):
AAATGATTCTGAAGAAAAATCGAGATGTGGTACAAATCCTAATGGGACATCAGAAAACTCTTC
Found at i:1106218 original size:117 final size:117
Alignment explanation
Indices: 1106012--1106229 Score: 364
Period size: 117 Copynumber: 1.9 Consensus size: 117
1106002 CTTCAAATGA
* * * * **
1106012 TTCTGAAGATAAATCGAGATGTGGTACAAATCCTAATGGGACATCAGAAAACTCTTCGACAGAGC
1 TTCTGAAGATAAAACGAGATGTGCTACAAATCCTAATGGGACATCAGAAAACTCGTCAACAGAAA
1106077 CGAAGGTGGATGATGAACTCACAAAACATTCTTGCAGGTCGACCGATGCTTC
66 CGAAGGTGGATGATGAACTCACAAAACATTCTTGCAGGTCGACCGATGCTTC
* *
1106129 TTCTGAAGATAAAACGAGATGTGCTACACATCCTAATGGGACATCAGAAATCTCGTCAACAGAAA
1 TTCTGAAGATAAAACGAGATGTGCTACAAATCCTAATGGGACATCAGAAAACTCGTCAACAGAAA
1106194 CGAAGGTGGATGATGAACTCACAAAACATTCTTGCA
66 CGAAGGTGGATGATGAACTCACAAAACATTCTTGCA
1106230 AGTCAACTAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 93 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (117 bp):
TTCTGAAGATAAAACGAGATGTGCTACAAATCCTAATGGGACATCAGAAAACTCGTCAACAGAAA
CGAAGGTGGATGATGAACTCACAAAACATTCTTGCAGGTCGACCGATGCTTC
Found at i:1115718 original size:22 final size:20
Alignment explanation
Indices: 1115693--1115749 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
1115683 AATTTTCAAA
*
1115693 TAATTAAAAAATAATTTTTAGT
1 TAATTAAAAAATAATATTT--T
*
1115715 TAA-TGAAAAATAATATTTT
1 TAATTAAAAAATAATATTTT
*
1115734 T-ATTAAAAAATTATAT
1 TAATTAAAAAATAATAT
1115750 ACATAGATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.03
19 13 0.43
21 13 0.43
22 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
TAATTAAAAAATAATATTTT
Found at i:1115942 original size:2 final size:2
Alignment explanation
Indices: 1115935--1115964 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1115925 TAATACTTTA
1115935 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1115965 ATTGATAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1118822 original size:16 final size:17
Alignment explanation
Indices: 1118795--1118833 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1118785 AAAAATATTT
1118795 TTATAA-GATAAA-TTG
1 TTATAATGATAAACTTG
1118810 TTATAATGATAAACTTG
1 TTATAATGATAAACTTG
*
1118827 TTGTAAT
1 TTATAAT
1118834 AATGAAGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 6 0.29
17 9 0.43
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (17 bp):
TTATAATGATAAACTTG
Found at i:1119631 original size:31 final size:31
Alignment explanation
Indices: 1119545--1119631 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
1119535 ATATTTGGAA
* *
1119545 AAAATTATAAATTAAACCCTTCAAATATTTTG
1 AAAATTTTAAATTAAGCCC-TCAAATATTTTG
* ** *
1119577 AAAATTTTAATTTAAGCTTTCAAATATTTTT
1 AAAATTTTAAATTAAGCCCTCAAATATTTTG
*
1119608 AAAGTTTTAAATT-AGCCCCTCAAA
1 AAAATTTTAAATTAAG-CCCTCAAA
1119632 CTTTATCACC
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
30 2 0.05
31 28 0.64
32 14 0.32
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.40
Consensus pattern (31 bp):
AAAATTTTAAATTAAGCCCTCAAATATTTTG
Found at i:1125569 original size:35 final size:35
Alignment explanation
Indices: 1125496--1125570 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1125486 CGTCACTAAC
*
1125496 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGATA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGACA
**
1125531 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGACA
1125566 AGTAA
1 AGTAA
1125571 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.29, G:0.27, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGACA
Found at i:1125715 original size:23 final size:23
Alignment explanation
Indices: 1125653--1125742 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
1125643 CATAATTCAA
1125653 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCATATCAGAATCCAG
* * *
1125677 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCATATCAGAATCCAG
1125701 GTCAATATCATATCAGAATCCAG
1 GTCAATATCATATCAGAATCCAG
** *
1125724 GTCAGGATCATAACAGAAT
1 GTCAATATCATATCAGAAT
1125743 TCAAGTCGGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
23 32 0.57
24 24 0.43
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (23 bp):
GTCAATATCATATCAGAATCCAG
Found at i:1128250 original size:15 final size:15
Alignment explanation
Indices: 1128230--1128272 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
1128220 GTGTCAACGT
*
1128230 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAA
1128245 GGGTCAACGGTCAAA
1 GGGTCAACGGTCAAA
1128260 GGGTCAACAGGTC
1 GGGTCAAC-GGTC
1128273 GGGTCGGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.28, C:0.23, G:0.35, T:0.14
Consensus pattern (15 bp):
GGGTCAACGGTCAAA
Found at i:1128251 original size:8 final size:8
Alignment explanation
Indices: 1128230--1128272 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
1128220 GTGTCAACGT
1128230 GGGTCAAC
1 GGGTCAAC
1128238 -GGTCAAC
1 GGGTCAAC
1128245 GGGTCAAC
1 GGGTCAAC
*
1128253 -GGTCAAA
1 GGGTCAAC
1128260 GGGTCAAC
1 GGGTCAAC
*
1128268 AGGTC
1 GGGTC
1128273 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 13 0.43
8 17 0.57
ACGTcount: A:0.28, C:0.23, G:0.35, T:0.14
Consensus pattern (8 bp):
GGGTCAAC
Found at i:1128283 original size:18 final size:18
Alignment explanation
Indices: 1128260--1128294 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1128250 AACGGTCAAA
1128260 GGGTCAACAGGTCGGGTC
1 GGGTCAACAGGTCGGGTC
*
1128278 GGGTCAACTGGTCGGGT
1 GGGTCAACAGGTCGGGT
1128295 AAACGGGTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.46, T:0.20
Consensus pattern (18 bp):
GGGTCAACAGGTCGGGTC
Found at i:1128290 original size:13 final size:13
Alignment explanation
Indices: 1128272--1128320 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
1128262 GTCAACAGGT
*
1128272 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
1128285 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
1128298 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1128311 CGGGTCGGGT
1 CGGGTCGGGT
1128321 CGGGTCGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1135228 original size:293 final size:293
Alignment explanation
Indices: 1134701--1135288 Score: 1140
Period size: 293 Copynumber: 2.0 Consensus size: 293
1134691 TAAATAGAAC
1134701 TATATAAAAAAAAACTGTTGCTCAGATAAATTATAGCTCATTCTACAGTAATCGAGTCTATGAAG
1 TATATAAAAAAAAACTGTTGCTCAGATAAATTATAGCTCATTCTACAGTAATCGAGTCTATGAAG
*
1134766 ATATATATATATGTAAAAGATCATAACCATCAATGAAAATGTCCTTTTCCTCTCTTCTTCTCACT
66 ATATATATATATGTAAAAGATCATAACCATCAATGAAAATGTCCTTTCCCTCTCTTCTTCTCACT
1134831 TTTGCCTGTCCATTCATTTCCTGCTATAATCACTCTCAGACTATGACACCTTGTATAATTGAACT
131 TTTGCCTGTCCATTCATTTCCTGCTATAATCACTCTCAGACTATGACACCTTGTATAATTGAACT
*
1134896 AAAAGATACACAACCAATGCAAAACGCAAATATTGCAGTCAATAAGATTGGATGATATTGAATCT
196 AAAAGATACACAACCAATGCAAAACACAAATATTGCAGTCAATAAGATTGGATGATATTGAATCT
1134961 TAAGGAAAATCATGACCCAGAGAAGACTGGAGA
261 TAAGGAAAATCATGACCCAGAGAAGACTGGAGA
1134994 TATATAAAAAAAAACTGTTGCTCAGATAAATTATAGCTCATTCTACAGTAATCGAGTCTATGAAG
1 TATATAAAAAAAAACTGTTGCTCAGATAAATTATAGCTCATTCTACAGTAATCGAGTCTATGAAG
1135059 ATATATATATATGTAAAAGATCATAACCATCAATGAAAATGTCCTTTCCCTCTCTTCTTCTCACT
66 ATATATATATATGTAAAAGATCATAACCATCAATGAAAATGTCCTTTCCCTCTCTTCTTCTCACT
1135124 TTTGCCTGTCCATTCATTTCCTGCTATAATCACTCTCAGACTATGACACCTTGTATAATTGAACT
131 TTTGCCTGTCCATTCATTTCCTGCTATAATCACTCTCAGACTATGACACCTTGTATAATTGAACT
*
1135189 AAAAGATACCCAACCAATGCAAAACACAAATATTGCAGTCAATAAGATTGGATGATATTGAATCT
196 AAAAGATACACAACCAATGCAAAACACAAATATTGCAGTCAATAAGATTGGATGATATTGAATCT
*
1135254 TAAGGAAAATCATGACCGAGAGAAGACTGGAGA
261 TAAGGAAAATCATGACCCAGAGAAGACTGGAGA
1135287 TA
1 TA
1135289 CAGTGTGTGT
Statistics
Matches: 291, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
293 291 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (293 bp):
TATATAAAAAAAAACTGTTGCTCAGATAAATTATAGCTCATTCTACAGTAATCGAGTCTATGAAG
ATATATATATATGTAAAAGATCATAACCATCAATGAAAATGTCCTTTCCCTCTCTTCTTCTCACT
TTTGCCTGTCCATTCATTTCCTGCTATAATCACTCTCAGACTATGACACCTTGTATAATTGAACT
AAAAGATACACAACCAATGCAAAACACAAATATTGCAGTCAATAAGATTGGATGATATTGAATCT
TAAGGAAAATCATGACCCAGAGAAGACTGGAGA
Found at i:1136535 original size:20 final size:19
Alignment explanation
Indices: 1136512--1136554 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1136502 ATACAAGGAG
*
1136512 AAAAAAAATAAA-AAATTAC
1 AAAAAAAA-AAACAAAATAC
1136531 AAAAAAAAAAACAAAATAC
1 AAAAAAAAAAACAAAATAC
1136550 AAAAA
1 AAAAA
1136555 CTTATTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.84, C:0.07, G:0.00, T:0.09
Consensus pattern (19 bp):
AAAAAAAAAAACAAAATAC
Found at i:1136785 original size:15 final size:15
Alignment explanation
Indices: 1136765--1136801 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1136755 CCAAGAAGGT
1136765 CGCCATGTATGCTGG
1 CGCCATGTATGCTGG
*
1136780 CGCCATGTGTGCTGG
1 CGCCATGTATGCTGG
1136795 CGCCATG
1 CGCCATG
1136802 CAGTGAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (15 bp):
CGCCATGTATGCTGG
Found at i:1138770 original size:107 final size:107
Alignment explanation
Indices: 1138659--1138853 Score: 284
Period size: 107 Copynumber: 1.8 Consensus size: 107
1138649 TTTCTATTAT
* * * * *
1138659 ATTTTAGTACCCACCATTAAAAACTTAACTCATTTAGTACCTAAACTAT-TAGTTTTGGTCGGTT
1 ATTTTAGCACCCACCATTAAAAACTTAACGCATTTAGTACCTAAACAATCTA-TTTTGATCCGTT
1138723 TTAGCACCTAAACTTTCAATTTTTAACGTTTAGTTTAGTTTTC
65 TTAGCACCTAAACTTTCAATTTTTAACGTTTAGTTTAGTTTTC
* * *
1138766 ATTTTAGCACCCGCCATTAAAAACTTAACGCGTTTAGTATCTAAACAATCTATTTTGATCCGTTT
1 ATTTTAGCACCCACCATTAAAAACTTAACGCATTTAGTACCTAAACAATCTATTTTGATCCGTTT
* *
1138831 TAGTACCTAAACTTTCTATTTTT
66 TAGCACCTAAACTTTCAATTTTT
1138854 TCGAAACTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
107 75 0.97
108 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (107 bp):
ATTTTAGCACCCACCATTAAAAACTTAACGCATTTAGTACCTAAACAATCTATTTTGATCCGTTT
TAGCACCTAAACTTTCAATTTTTAACGTTTAGTTTAGTTTTC
Found at i:1139950 original size:18 final size:18
Alignment explanation
Indices: 1139927--1139961 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1139917 ATAGTATTAA
*
1139927 ATCGCGGTTGTGGTGTCC
1 ATCGCGGTTGCGGTGTCC
1139945 ATCGCGGTTGCGGTGTC
1 ATCGCGGTTGCGGTGTC
1139962 GTGATTGCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.23, G:0.40, T:0.31
Consensus pattern (18 bp):
ATCGCGGTTGCGGTGTCC
Found at i:1142234 original size:19 final size:20
Alignment explanation
Indices: 1142192--1142234 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1142182 GGTTGAAAAA
* *
1142192 AAAGTAAAGTATCTATACCT
1 AAAGCAAAGTATCAATACCT
1142212 AAAGCAAAGTATCAATA-CT
1 AAAGCAAAGTATCAATACCT
1142231 AAAG
1 AAAG
1142235 GGTTAATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (20 bp):
AAAGCAAAGTATCAATACCT
Found at i:1142264 original size:20 final size:20
Alignment explanation
Indices: 1142219--1142270 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1142209 CCTAAAGCAA
*
1142219 AGTATCAATACTAAAGGGTT
1 AGTATCAATACTAAAAGGTT
* *
1142239 AATATCGATACTAAAAGGTT
1 AGTATCAATACTAAAAGGTT
* *
1142259 CGTATCAGTACT
1 AGTATCAATACT
1142271 GACCCTTTAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTATCAATACTAAAAGGTT
Found at i:1144083 original size:65 final size:66
Alignment explanation
Indices: 1144001--1144125 Score: 180
Period size: 65 Copynumber: 1.9 Consensus size: 66
1143991 TTTAATATTC
* *
1144001 TAATTTCATTCTCAAATTATGACCCTCATACTAAATTGATCCCTAAACTTTGAA-TATTCTTTGT
1 TAATTTCATCCTCAAATTATGACCATCATACTAAATTGATCCCTAAACTTTGAATTATTCTTTGT
1144065 T
66 T
* * * * *
1144066 TAATTTCATCCTTAAATTATGTCCATCATTCTAAATTGGTCCCTAAACTTTTAATTATTC
1 TAATTTCATCCTCAAATTATGACCATCATACTAAATTGATCCCTAAACTTTGAATTATTC
1144126 CAATTTAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
65 47 0.90
66 5 0.10
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (66 bp):
TAATTTCATCCTCAAATTATGACCATCATACTAAATTGATCCCTAAACTTTGAATTATTCTTTGT
T
Found at i:1144556 original size:27 final size:27
Alignment explanation
Indices: 1144518--1144571 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1144508 CTTAAATTGA
1144518 GATAAAGTTAGTCGTCGATATGTTGTC
1 GATAAAGTTAGTCGTCGATATGTTGTC
*
1144545 GATAAAGTTAGTTGTCGATATGTTGTC
1 GATAAAGTTAGTCGTCGATATGTTGTC
1144572 ATGTTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (27 bp):
GATAAAGTTAGTCGTCGATATGTTGTC
Found at i:1145601 original size:15 final size:15
Alignment explanation
Indices: 1145583--1145611 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1145573 CTCCTCTATT
1145583 GCTTTCACCTCTGGC
1 GCTTTCACCTCTGGC
1145598 GCTTTCACCTCTGG
1 GCTTTCACCTCTGG
1145612 GCGATTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.38, G:0.21, T:0.34
Consensus pattern (15 bp):
GCTTTCACCTCTGGC
Found at i:1146448 original size:94 final size:95
Alignment explanation
Indices: 1146278--1146449 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 95
1146268 ATATTTAAGA
* *
1146278 AGTATTCTGTCAATTCTCAACAACCAAAACCATATAACAAACCAGCATATTTCTCAGTCCACCAG
1 AGTACTCTGTCAATTCTCAACAACCAAAACCATATAACAAACCAGCATATTTCTCAGTCAACCAG
*
1146343 CTAAAGGAATTTTTCGTTGAATCATTACAG
66 CTAAAGAAATTTTTCGTTGAATCATTACAG
* * * * * *
1146373 AGTACTCTGTCCATTCTCAAC-ACCAAGACCGTATAACACACCGGCATATTTCTCTGTCGAACCA
1 AGTACTCTGTCAATTCTCAACAACCAAAACCATATAACAAACCAGCATATTTCTCAGTC-AACCA
*
1146437 -CTAGAGAAATTTT
65 GCTAAAGAAATTTT
1146450 CTCTCAGTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
94 43 0.65
95 23 0.35
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (95 bp):
AGTACTCTGTCAATTCTCAACAACCAAAACCATATAACAAACCAGCATATTTCTCAGTCAACCAG
CTAAAGAAATTTTTCGTTGAATCATTACAG
Found at i:1148877 original size:139 final size:131
Alignment explanation
Indices: 1148665--1148942 Score: 394
Period size: 139 Copynumber: 2.1 Consensus size: 131
1148655 TTATCAAATG
* * *
1148665 AAATTAATGTCGTTGACATCTCGAGCACTTAAAGTGATCACGTTTGTAACATTAGGTACATGAAT
1 AAATTAATGTCGTTGACATCTCGAGCACTTAAAGTGATCACGTTTATAACATTAGGCACATAAAT
*
1148730 GTGTCAAAAAATACCGTAGACACCTATTCAACACAAAAAATATAGTTTAGACATTTATTTAAACA
66 GTGTCAAAAAATACC-TAGACA---A--CAA-A-AAAAAATATAATTTAGACATTTATTTAAACA
*
1148795 TTAAACCTT
123 TTAAACCTC
*
1148804 AAATTAATGTCGTTGACATCTTGAGCACTTAAAGTGATCACGTTTATAACATTAGGCACATAAAT
1 AAATTAATGTCGTTGACATCTCGAGCACTTAAAGTGATCACGTTTATAACATTAGGCACATAAAT
** * *
1148869 GTGTCAAAAAATACCTATTCAACAAAAAAAAATATAATTTAGACATTTATTTAAGCATTAAATCT
66 GTGTCAAAAAATACCTAGACAACAAAAAAAAATATAATTTAGACATTTATTTAAACATTAAACCT
1148934 C
131 C
1148935 AAATTAAT
1 AAATTAAT
1148943 TGATCTAATG
Statistics
Matches: 129, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
131 44 0.34
132 1 0.01
133 3 0.02
135 1 0.01
138 4 0.03
139 76 0.59
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.32
Consensus pattern (131 bp):
AAATTAATGTCGTTGACATCTCGAGCACTTAAAGTGATCACGTTTATAACATTAGGCACATAAAT
GTGTCAAAAAATACCTAGACAACAAAAAAAAATATAATTTAGACATTTATTTAAACATTAAACCT
C
Found at i:1149661 original size:3 final size:3
Alignment explanation
Indices: 1149653--1149683 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1149643 GAAATAAACA
1149653 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1149684 CGGGATTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1150388 original size:6 final size:6
Alignment explanation
Indices: 1150377--1150428 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
1150367 CTAATCTCCT
* * * *
1150377 TTTTTA TTTTTA TTATTA TTTTTA TTTTTA TTTATA TTTTTA CTTCTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1150425 TTTT
1 TTTT
1150429 CAAAATTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:1156143 original size:20 final size:20
Alignment explanation
Indices: 1156118--1156166 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1156108 CATTTAAGAT
1156118 GTATCGATATTGGTCTCTAG
1 GTATCGATATTGGTCTCTAG
1156138 GTATCGATATTGGTCTCTAG
1 GTATCGATATTGGTCTCTAG
1156158 GTATCGATA
1 GTATCGATA
1156167 CTCAAGGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.39
Consensus pattern (20 bp):
GTATCGATATTGGTCTCTAG
Found at i:1160592 original size:2 final size:2
Alignment explanation
Indices: 1160585--1160611 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1160575 TCTTAGTTTC
1160585 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 T
1160612 GTTCTATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1166551 original size:54 final size:54
Alignment explanation
Indices: 1166469--1166691 Score: 263
Period size: 54 Copynumber: 4.1 Consensus size: 54
1166459 AGAATCTCCA
* *
1166469 AAACAAAATCTGGTCCACA-AATCTGTTTTGCCAGAACCATCACCAAGTTTTCTG
1 AAACAAAATCTGGTCCA-ATAATCTGTTTTGCCAGAACCATCACCAACTTCTCTG
* *
1166523 AAACAAAATCCGGTCC-ATGAATCTGTTTTGCCAGAACCATCACCAAGTTCTCTG
1 AAACAAAATCTGGTCCAAT-AATCTGTTTTGCCAGAACCATCACCAACTTCTCTG
* * * * **
1166577 AAACAAAATCTGATCCAATTATCTGTTATGCCAGAACCGTCACCAACTTCTCCA
1 AAACAAAATCTGGTCCAATAATCTGTTTTGCCAGAACCATCACCAACTTCTCTG
* * * * *
1166631 AAACAAAATCAT-CTCCAATTATCTGTTTTGCCTGAACCGTCACCAACCTCTCTG
1 AAACAAAATC-TGGTCCAATAATCTGTTTTGCCAGAACCATCACCAACTTCTCTG
1166685 AAACAAA
1 AAACAAA
1166692 GTCATTCAGA
Statistics
Matches: 149, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
52 1 0.01
54 145 0.97
55 3 0.02
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.26
Consensus pattern (54 bp):
AAACAAAATCTGGTCCAATAATCTGTTTTGCCAGAACCATCACCAACTTCTCTG
Found at i:1176036 original size:47 final size:47
Alignment explanation
Indices: 1175996--1176085 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 47
1175986 AAATTCACTA
*
1175996 AATAATAAACCCATTCGCTTGAATTAAGTAATAAACAAAATAATAAT
1 AATAATAAAACCATTCGCTTGAATTAAGTAATAAACAAAATAATAAT
* * *
1176043 AATAATAAAACTATTCTCTTGAATTAAGTAATAAACAACATAA
1 AATAATAAAACCATTCGCTTGAATTAAGTAATAAACAAAATAA
1176086 ACAAAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (47 bp):
AATAATAAAACCATTCGCTTGAATTAAGTAATAAACAAAATAATAAT
Found at i:1182322 original size:16 final size:17
Alignment explanation
Indices: 1182301--1182337 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
1182291 TATAATATTT
1182301 ATATTTTAAT-TTTATG
1 ATATTTTAATATTTATG
1182317 ATATTTTAATATTTATG
1 ATATTTTAATATTTATG
1182334 ATAT
1 ATAT
1182338 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
ATATTTTAATATTTATG
Found at i:1183019 original size:2 final size:2
Alignment explanation
Indices: 1183012--1183075 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1183002 TTTATATTTG
1183012 AT AT AT AT AT 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 AT AT AT AT AT
1183054 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1183076 TATTTTAACA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1183912 original size:44 final size:43
Alignment explanation
Indices: 1183846--1184046 Score: 194
Period size: 44 Copynumber: 4.6 Consensus size: 43
1183836 TTATGAAACA
* * *
1183846 GAAAAAATTAGGGGTCTCAATTATAAAGGTAGAAAGTGAGATT
1 GAAAAAATTATGGGACTCAATTATAAAGGTAGAAAGTAAGATT
* *
1183889 GAAAAAACTTATGGGACTTAATTATAAAAGTAGAAAGTAAGATT
1 GAAAAAA-TTATGGGACTCAATTATAAAGGTAGAAAGTAAGATT
* * * * * *
1183933 GAAAATGATTATGGGCCTCAGTTGTAAAGGTAAAAAGTGAGATT
1 GAAAA-AATTATGGGACTCAATTATAAAGGTAGAAAGTAAGATT
* *
1183977 -AAAAAACTA-GGGACATCAATTATGAAGGTAGAAAGTAAGATT
1 GAAAAAATTATGGGAC-TCAATTATAAAGGTAGAAAGTAAGATT
*
1184019 -AAAATAATT-TAGGAGTCTCAATTATAAA
1 GAAAA-AATTAT-GG-GACTCAATTATAAA
1184047 ATTTTAAAAT
Statistics
Matches: 127, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
41 4 0.03
42 29 0.23
43 14 0.11
44 77 0.61
45 3 0.02
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.26
Consensus pattern (43 bp):
GAAAAAATTATGGGACTCAATTATAAAGGTAGAAAGTAAGATT
Found at i:1184099 original size:43 final size:43
Alignment explanation
Indices: 1184052--1184229 Score: 148
Period size: 43 Copynumber: 4.1 Consensus size: 43
1184042 ATAAAATTTT
* * * *
1184052 AAAATGTAATTAAAAAAATTAGAGGCCTCGATTATAAAGGCAA
1 AAAATGAAATTAAAAAAATTAGAGACCTCAATTATAAAGACAA
* * * *
1184095 AAAATGGAATTGAAAAAATTAGAGACTTCAATTATAAAGATAA
1 AAAATGAAATTAAAAAAATTAGAGACCTCAATTATAAAGACAA
* * * *
1184138 AAAGTGAAATTAAGAAAA--A-CGACCTCAATTATAAAGATAA
1 AAAATGAAATTAAAAAAATTAGAGACCTCAATTATAAAGACAA
* * * *
1184178 AAAATAAAAGATTTAAAAAAATTAGAGACC-CTAATTAAAAATATAA
1 AAAAT-GAA-A-TTAAAAAAATTAGAGACCTC-AATTATAAAGACAA
1184224 AAAATG
1 AAAATG
1184230 GGAGCCTTAA
Statistics
Matches: 108, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
40 23 0.21
41 3 0.03
42 1 0.01
43 58 0.54
45 2 0.02
46 21 0.19
ACGTcount: A:0.57, C:0.07, G:0.12, T:0.23
Consensus pattern (43 bp):
AAAATGAAATTAAAAAAATTAGAGACCTCAATTATAAAGACAA
Found at i:1184595 original size:2 final size:2
Alignment explanation
Indices: 1184588--1184616 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1184578 CTATTTTACT
1184588 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 T
1184617 TGAATCAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1184702 original size:22 final size:22
Alignment explanation
Indices: 1184671--1184720 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1184661 TTAGTTAGGC
*
1184671 TGTTAATAATCAGTTAGGTTGT
1 TGTTAATAATCAGTTAGATTGT
* *
1184693 TGTTATTAATTAGTTAGATTGT
1 TGTTAATAATCAGTTAGATTGT
1184715 TAGTTA
1 T-GTTA
1184721 GGCTAGTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.50
Consensus pattern (22 bp):
TGTTAATAATCAGTTAGATTGT
Found at i:1191527 original size:23 final size:23
Alignment explanation
Indices: 1191481--1191527 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1191471 GAACAGATGT
**
1191481 ACGAATATGTTTGTGAACGTTAA
1 ACGAATATGTTTGTGAACACTAA
*
1191504 ACGAATATGTTTGTGAATACTAA
1 ACGAATATGTTTGTGAACACTAA
1191527 A
1 A
1191528 AAGATGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (23 bp):
ACGAATATGTTTGTGAACACTAA
Found at i:1193750 original size:23 final size:23
Alignment explanation
Indices: 1193724--1193774 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1193714 TGGAAGCAAC
* **
1193724 TGACTGAACCTTCTGGAAGTTGT
1 TGACTGAACCTTCTAGAAACTGT
*
1193747 TGACTGAATCTTCTAGAAACTGT
1 TGACTGAACCTTCTAGAAACTGT
1193770 TGACT
1 TGACT
1193775 CGCTGCCACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (23 bp):
TGACTGAACCTTCTAGAAACTGT
Found at i:1193855 original size:34 final size:34
Alignment explanation
Indices: 1193812--1193881 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
1193802 AATTCATGAC
* *
1193812 CACTCTTCCAACATTGATTCTTGAACAAAAAATA
1 CACTATTCCAACATTGATTCCTGAACAAAAAATA
1193846 CACTATTCCAACATTGATTCCTGAACAAAAAATA
1 CACTATTCCAACATTGATTCCTGAACAAAAAATA
1193880 CA
1 CA
1193882 GTTTTTAGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (34 bp):
CACTATTCCAACATTGATTCCTGAACAAAAAATA
Found at i:1209976 original size:11 final size:11
Alignment explanation
Indices: 1209960--1210007 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
1209950 ATTGAATATA
1209960 TAAACGAACAC
1 TAAACGAACAC
1209971 TAAACGAACAC
1 TAAACGAACAC
** *
1209982 TAAATAAACAT
1 TAAACGAACAC
*
1209993 TAAACGGACAC
1 TAAACGAACAC
1210004 TAAA
1 TAAA
1210008 TAAACCCTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.56, C:0.21, G:0.08, T:0.15
Consensus pattern (11 bp):
TAAACGAACAC
Found at i:1209991 original size:22 final size:22
Alignment explanation
Indices: 1209966--1210018 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1209956 TATATAAACG
1209966 AACACTAAACGAACACTAAATA
1 AACACTAAACGAACACTAAATA
* *
1209988 AACATTAAACGGACACTAAATA
1 AACACTAAACGAACACTAAATA
*
1210010 AACCCTAAA
1 AACACTAAA
1210019 TAAATATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.57, C:0.23, G:0.06, T:0.15
Consensus pattern (22 bp):
AACACTAAACGAACACTAAATA
Found at i:1209998 original size:33 final size:34
Alignment explanation
Indices: 1209957--1210045 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 34
1209947 AAAATTGAAT
1209957 ATATAAACGAACACTAAACGAACACTAAATAAAC
1 ATATAAACGAACACTAAACGAACACTAAATAAAC
* ** * *
1209991 AT-TAAACGGACACTAAATAAACCCTAAATAAAT
1 ATATAAACGAACACTAAACGAACACTAAATAAAC
** *
1210024 ATATTTACGAACATTAAACGAA
1 ATATAAACGAACACTAAACGAA
1210046 TATATTCACG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
33 28 0.65
34 15 0.35
ACGTcount: A:0.55, C:0.18, G:0.07, T:0.20
Consensus pattern (34 bp):
ATATAAACGAACACTAAACGAACACTAAATAAAC
Found at i:1210041 original size:23 final size:23
Alignment explanation
Indices: 1210015--1210068 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1210005 AAATAAACCC
* *
1210015 TAAATAAATATATTTACGAACAT
1 TAAATAAATATATTCACGAACAA
**
1210038 TAAACGAATATATTCACGAACAA
1 TAAATAAATATATTCACGAACAA
1210061 TAAATAAA
1 TAAATAAA
1210069 CAAAAACAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (23 bp):
TAAATAAATATATTCACGAACAA
Found at i:1214397 original size:162 final size:162
Alignment explanation
Indices: 1214130--1214451 Score: 608
Period size: 162 Copynumber: 2.0 Consensus size: 162
1214120 ATCAGAAAAC
*
1214130 ATTTATGGCTTATTTCTCATTCTTTCTTACCTCGTAAAGCGTGCGTGACATCAAAACTCCATAAA
1 ATTTATGGCTTATTTCTCATTCTTTCTTACCTCGTAAAGCGTGCGTGAAATCAAAACTCCATAAA
1214195 TCCAAGACGAAGCTCAATGAAAGAAATTAGTGAAGAAAATCGAAAGAATCTGAGGAGGGAAAAGA
66 TCCAAGACGAAGCTCAATGAAAGAAATTAGTGAAGAAAATCGAAAGAATCTGAGGAGGGAAAAGA
*
1214260 AGAAAGTGAAGATAAACAGCGAAGATTAGAAA
131 AGAAAGTAAAGATAAACAGCGAAGATTAGAAA
1214292 ATTTATGGCTTATTTCTCATTCTTTCTTACCTCGTAAAGCGTGCGTGAAATCAAAACTCCATAAA
1 ATTTATGGCTTATTTCTCATTCTTTCTTACCTCGTAAAGCGTGCGTGAAATCAAAACTCCATAAA
* *
1214357 TCCAAGACGAAGCTCAATGAAAGAAATTTGTGAAGAAAATCGAAAGGATCTGAGGAGGGAAAAGA
66 TCCAAGACGAAGCTCAATGAAAGAAATTAGTGAAGAAAATCGAAAGAATCTGAGGAGGGAAAAGA
1214422 AGAAAGTAAAGATAAACAGCGAAGATTAGA
131 AGAAAGTAAAGATAAACAGCGAAGATTAGA
1214452 GGATTTAGGG
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
162 156 1.00
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (162 bp):
ATTTATGGCTTATTTCTCATTCTTTCTTACCTCGTAAAGCGTGCGTGAAATCAAAACTCCATAAA
TCCAAGACGAAGCTCAATGAAAGAAATTAGTGAAGAAAATCGAAAGAATCTGAGGAGGGAAAAGA
AGAAAGTAAAGATAAACAGCGAAGATTAGAAA
Found at i:1215389 original size:21 final size:21
Alignment explanation
Indices: 1215365--1215412 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1215355 CTTAACAATT
1215365 ATTTTATAACCATTCGATAAA
1 ATTTTATAACCATTCGATAAA
* * **
1215386 ATTTAATAATCATTTTATAAA
1 ATTTTATAACCATTCGATAAA
1215407 ATTTTA
1 ATTTTA
1215413 AGTTTGAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTTTATAACCATTCGATAAA
Found at i:1215997 original size:14 final size:15
Alignment explanation
Indices: 1215978--1216009 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1215968 TATCAGAATA
1215978 ATTTATTT-AATATT
1 ATTTATTTCAATATT
1215992 ATTTATTTCAATATT
1 ATTTATTTCAATATT
1216007 ATT
1 ATT
1216010 ATTAAAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTATTTCAATATT
Found at i:1216106 original size:22 final size:22
Alignment explanation
Indices: 1216073--1216150 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
1216063 ATTAAAATAA
1216073 ATTT-TTATAAATTATATTAATT
1 ATTTATTA-AAATTATATTAATT
* * *
1216095 ATTTATTAAAATGAGACTAA-T
1 ATTTATTAAAATTATATTAATT
*
1216116 A-TTACT--AATTATATTAATT
1 ATTTATTAAAATTATATTAATT
*
1216135 ACTTATTAAAATTATA
1 ATTTATTAAAATTATA
1216151 ATATTAAAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
18 8 0.19
19 2 0.05
20 8 0.19
21 2 0.05
22 20 0.47
23 3 0.07
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (22 bp):
ATTTATTAAAATTATATTAATT
Found at i:1216390 original size:15 final size:17
Alignment explanation
Indices: 1216356--1216419 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 17
1216346 TTAAAACTAT
1216356 TATTAAATATAATTTAAA
1 TATTAAATAT-ATTTAAA
1216374 TATTAAATAT-TTTAATA
1 TATTAAATATATTTAA-A
1216391 TGATACTAAATAATATATT-AA
1 T-AT--TAAAT-ATAT-TTAAA
1216412 TATTAAAT
1 TATTAAAT
1216420 GTATAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
16 5 0.13
17 2 0.05
18 17 0.44
20 7 0.18
21 4 0.10
22 2 0.05
23 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TATTAAATATATTTAAA
Found at i:1216735 original size:3 final size:3
Alignment explanation
Indices: 1216727--1216764 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1216717 ACATAGAAAT
1216727 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1216765 TCACATCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1217294 original size:25 final size:25
Alignment explanation
Indices: 1217265--1217314 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1217255 ATTTAAACCG
* *
1217265 AAACCGAATTGATAAAAAATCGAAA
1 AAACCGAATGGATAAAAAACCGAAA
*
1217290 AAACCGAATGGTTAAAAAACCGAAA
1 AAACCGAATGGATAAAAAACCGAAA
1217315 CCGGTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (25 bp):
AAACCGAATGGATAAAAAACCGAAA
Found at i:1219842 original size:31 final size:31
Alignment explanation
Indices: 1219772--1219848 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
1219762 TTCAACGTCC
*
1219772 AAGTGACCAAAACTTAATAAAATGATAATAT
1 AAGTGACCAAAACTTAATAAAATGATAACAT
* * * *
1219803 AAGGGACCAGAACTTAAT-AAATCGATAGCGT
1 AAGTGACCAAAACTTAATAAAAT-GATAACAT
1219834 AAGTGACCAAAACTT
1 AAGTGACCAAAACTT
1219849 GTGTTTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAATGATAACAT
Found at i:1222362 original size:18 final size:19
Alignment explanation
Indices: 1222339--1222381 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1222329 CAGCAGCACA
*
1222339 TAACTGCTC-TTAACAAGC
1 TAACTGCTCATTAACAAAC
1222357 TAACTGCTCATTTAACAAAC
1 TAACTGCTCA-TTAACAAAC
1222377 TAACT
1 TAACT
1222382 ACCATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (19 bp):
TAACTGCTCATTAACAAAC
Found at i:1222389 original size:19 final size:20
Alignment explanation
Indices: 1222348--1222389 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1222338 ATAACTGCTC
* *
1222348 TTAACAAGCTAACTGCTCAT
1 TTAACAAACTAACTACTCAT
1222368 TTAACAAACTAACTAC-CAT
1 TTAACAAACTAACTACTCAT
1222387 TTA
1 TTA
1222390 GTAGCTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (20 bp):
TTAACAAACTAACTACTCAT
Found at i:1224391 original size:63 final size:63
Alignment explanation
Indices: 1224287--1224410 Score: 180
Period size: 63 Copynumber: 2.0 Consensus size: 63
1224277 TATTAATCAT
*
1224287 CTCGTCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
1 CTCGGCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
* * *
1224350 CTCGGCTTCATTATGTACTT-CTGCATTAC-CATCTTCTTCATGCACGGTGGTGGTATTTGGT
1 CTCGGCTTCATTATG-AATTGCTGCATTACTCA-CTTCTTCATGCACGGTGATGATATTTGGT
1224411 AACTGACTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.91
64 3 0.05
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (63 bp):
CTCGGCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
Found at i:1226991 original size:18 final size:19
Alignment explanation
Indices: 1226968--1227010 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1226958 CAGCAGCACA
*
1226968 TAACTGCTC-TTAACAAGC
1 TAACTGCTCATTAACAAAC
1226986 TAACTGCTCATTTAACAAAC
1 TAACTGCTCA-TTAACAAAC
1227006 TAACT
1 TAACT
1227011 ACCATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (19 bp):
TAACTGCTCATTAACAAAC
Found at i:1227018 original size:19 final size:20
Alignment explanation
Indices: 1226977--1227018 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1226967 ATAACTGCTC
* *
1226977 TTAACAAGCTAACTGCTCAT
1 TTAACAAACTAACTACTCAT
1226997 TTAACAAACTAACTAC-CAT
1 TTAACAAACTAACTACTCAT
1227016 TTA
1 TTA
1227019 GTAGCTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (20 bp):
TTAACAAACTAACTACTCAT
Found at i:1229421 original size:18 final size:19
Alignment explanation
Indices: 1229386--1229422 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1229376 CAGGGAATGT
1229386 AAGATTATCAGTGAGAATAA
1 AAGATTATCAG-GAGAATAA
1229406 AAGATTATCA-GAGAATA
1 AAGATTATCAGGAGAATA
1229423 GAAATACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGAGAATAA
Found at i:1229996 original size:43 final size:44
Alignment explanation
Indices: 1229949--1230085 Score: 133
Period size: 43 Copynumber: 3.2 Consensus size: 44
1229939 TTACAACATA
*
1229949 TAGCGGCGATTGT-TCA-ACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGATT-TATCATACAAACGCCGCAATAGGTATTGATATT
*
1229992 TAGCGGCG-TTTATCATTA-AAACGCCGCAATAGGTTTTGATATT
1 TAGCGGCGATTTATCA-TACAAACGCCGCAATAGGTATTGATATT
* ** * * *
1230035 TAACGGC-ATTTGGCAGACAAACGCCGCAATA-GTCGTTGATGTT
1 TAGCGGCGATTTATCATACAAACGCCGCAATAGGT-ATTGATATT
1230078 TAGCGGCG
1 TAGCGGCG
1230086 TTTTCTTCCA
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
41 1 0.01
42 8 0.10
43 68 0.87
44 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
TAGCGGCGATTTATCATACAAACGCCGCAATAGGTATTGATATT
Found at i:1230589 original size:21 final size:21
Alignment explanation
Indices: 1230525--1230633 Score: 103
Period size: 21 Copynumber: 5.2 Consensus size: 21
1230515 TGATACATTA
* * *
1230525 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
1230546 CCTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
1230567 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* **
1230588 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* *
1230609 CTGCTCTCTCTGTTTCC-CTTG
1 CTTCTCTCTCTGCTTCCGC-TG
1230630 CTTC
1 CTTC
1230634 ATTTTCCGCT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
20 1 0.01
21 74 0.99
ACGTcount: A:0.01, C:0.40, G:0.18, T:0.40
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:1239218 original size:41 final size:43
Alignment explanation
Indices: 1239168--1239262 Score: 115
Period size: 41 Copynumber: 2.3 Consensus size: 43
1239158 TTTGTGGTAT
* * * *
1239168 AAACGCCGCTAATTTG-CCACCCTATTGCGGCATTTTT-GTAA
1 AAACGCCGCTAATATGTCAACCCTATTGCAGCATTTTTACTAA
* *
1239209 AAACGCCGCT-ATATGTCAACTCTATTGCAGCGTTTTTACTAA
1 AAACGCCGCTAATATGTCAACCCTATTGCAGCATTTTTACTAA
1239251 AAACGCCGCTAA
1 AAACGCCGCTAA
1239263 AGTATCAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 4 0.09
41 27 0.60
42 13 0.29
43 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAATATGTCAACCCTATTGCAGCATTTTTACTAA
Found at i:1240017 original size:24 final size:24
Alignment explanation
Indices: 1239972--1240018 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1239962 TTTATGTCCG
* * *
1239972 TTCATTTATGTTCCTTCGTTTATT
1 TTCATTTATGTGCATTCATTTATT
*
1239996 TTCATTTATGTGCATTTATTTAT
1 TTCATTTATGTGCATTCATTTAT
1240019 GTTTAGCTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.13, G:0.09, T:0.62
Consensus pattern (24 bp):
TTCATTTATGTGCATTCATTTATT
Found at i:1240193 original size:10 final size:10
Alignment explanation
Indices: 1240178--1240223 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
1240168 GGAAAGAAAA
*
1240178 ATTTATTTTC
1 ATTTATGTTC
1240188 ATTTATGTTC
1 ATTTATGTTC
* *
1240198 GTTTACGTTC
1 ATTTATGTTC
*
1240208 GTTTATGTTC
1 ATTTATGTTC
1240218 ATTTAT
1 ATTTAT
1240224 TGTGTTCGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (10 bp):
ATTTATGTTC
Found at i:1240235 original size:13 final size:12
Alignment explanation
Indices: 1240204--1240330 Score: 58
Period size: 10 Copynumber: 10.8 Consensus size: 12
1240194 GTTCGTTTAC
1240204 GTTCGTTTA--T
1 GTTCGTTTATTT
*
1240214 GTTCATTTATTGT
1 GTTCGTTTATT-T
1240227 GTTCGTTTACGTTT
1 GTTCGTTTA--TTT
*
1240241 GTTCGTTTA--C
1 GTTCGTTTATTT
*
1240251 GTTCGTTAATTGT
1 GTTCGTTTATT-T
1240264 GTTCGTTTA--T
1 GTTCGTTTATTT
**
1240274 GTTCGTTTACATCC
1 GTTCGTTT--ATTT
*
1240288 GTTCGTTTA--C
1 GTTCGTTTATTT
1240298 GTTCGTTTATTGT
1 GTTCGTTTATT-T
*
1240311 GTTCATTTA--T
1 GTTCGTTTATTT
1240321 GTTCGTTTAT
1 GTTCGTTTAT
1240331 ATCCGTTTGT
Statistics
Matches: 91, Mismatches: 10, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
10 44 0.48
12 2 0.02
13 25 0.27
14 18 0.20
15 2 0.02
ACGTcount: A:0.12, C:0.13, G:0.19, T:0.56
Consensus pattern (12 bp):
GTTCGTTTATTT
Found at i:1240245 original size:14 final size:14
Alignment explanation
Indices: 1240226--1240253 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1240216 TCATTTATTG
1240226 TGTTCGTTTACGTT
1 TGTTCGTTTACGTT
1240240 TGTTCGTTTACGTT
1 TGTTCGTTTACGTT
1240254 CGTTAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.21, T:0.57
Consensus pattern (14 bp):
TGTTCGTTTACGTT
Found at i:1240277 original size:47 final size:46
Alignment explanation
Indices: 1240193--1240368 Score: 178
Period size: 47 Copynumber: 3.7 Consensus size: 46
1240183 TTTTCATTTA
* * *
1240193 TGTTCGTTTACGTTCG-T-TTATGTTCATTTATTGTGTTCGTTTACGTT
1 TGTTCGTTTACGTTCGTTATTGTGTTCATTTA---TGTTCGTTTACATC
*
1240240 TGTTCGTTTACGTTCGTTAATTGTGTTCGTTTATGTTCGTTTACATC
1 TGTTCGTTTACGTTCGTT-ATTGTGTTCATTTATGTTCGTTTACATC
* *
1240287 CGTTCGTTTACGTTCGTTTATTGTGTTCATTTATGTTCGTTTATATC
1 TGTTCGTTTACGTTCG-TTATTGTGTTCATTTATGTTCGTTTACATC
* * *
1240334 CGTTTGTTTATC-TTCGTTCATTTGTGTTCGTTTAT
1 TGTTCGTTTA-CGTTCGTT-A-TTGTGTTCATTTAT
1240369 CATTTAAATG
Statistics
Matches: 113, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
46 2 0.02
47 83 0.73
48 17 0.15
50 11 0.10
ACGTcount: A:0.11, C:0.14, G:0.18, T:0.56
Consensus pattern (46 bp):
TGTTCGTTTACGTTCGTTATTGTGTTCATTTATGTTCGTTTACATC
Found at i:1240295 original size:24 final size:23
Alignment explanation
Indices: 1240241--1240351 Score: 98
Period size: 24 Copynumber: 4.7 Consensus size: 23
1240231 GTTTACGTTT
* **
1240241 GTTCGTTTACGTTCG-TTAATTGT
1 GTTCGTTTATGTTCGTTTAA-TCC
1240264 GTTCGTTTATGTTCGTTTACATCC
1 GTTCGTTTATGTTCGTTTA-ATCC
* * **
1240288 GTTCGTTTACGTTCGTTTATTGT
1 GTTCGTTTATGTTCGTTTAATCC
*
1240311 GTTCATTTATGTTCGTTTATATCC
1 GTTCGTTTATGTTCGTTTA-ATCC
* *
1240335 GTTTGTTTATCTTCGTT
1 GTTCGTTTATGTTCGTT
1240352 CATTTGTGTT
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
23 32 0.46
24 37 0.53
25 1 0.01
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTTAATCC
Found at i:1240304 original size:14 final size:14
Alignment explanation
Indices: 1240227--1240257 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1240217 CATTTATTGT
*
1240227 GTTCGTTTACGTTT
1 GTTCGTTTACGTTC
1240241 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
1240255 GTT
1 GTT
1240258 AATTGTGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.16, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGTTTACGTTC
Found at i:1240366 original size:24 final size:24
Alignment explanation
Indices: 1240240--1240369 Score: 97
Period size: 24 Copynumber: 5.5 Consensus size: 24
1240230 CGTTTACGTT
*
1240240 TGTTCGTTTA-CGTTCG-TTAATTG
1 TGTTCGTTTATC-TTCGTTTATTTG
* ** *
1240263 TGTTCGTTTATGTTCGTTTACATC
1 TGTTCGTTTATCTTCGTTTATTTG
*
1240287 CGTTCGTTTA-CGTTCGTTTA-TTG
1 TGTTCGTTTATC-TTCGTTTATTTG
* * * *
1240310 TGTTCATTTATGTTCGTTTATATC
1 TGTTCGTTTATCTTCGTTTATTTG
* * *
1240334 CGTTTGTTTATCTTCGTTCATTTG
1 TGTTCGTTTATCTTCGTTTATTTG
1240358 TGTTCGTTTATC
1 TGTTCGTTTATC
1240370 ATTTAAATGA
Statistics
Matches: 80, Mismatches: 22, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
23 31 0.39
24 49 0.61
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.55
Consensus pattern (24 bp):
TGTTCGTTTATCTTCGTTTATTTG
Found at i:1244274 original size:18 final size:19
Alignment explanation
Indices: 1244223--1244274 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
1244213 TTTAATATTT
*
1244223 TTATTATCTATTAA-TAAA
1 TTATTATTTATTAATTAAA
*
1244241 TTATTAATTATTAATTAAA
1 TTATTATTTATTAATTAAA
1244260 TT-TTATTTATTAATT
1 TTATTATTTATTAATT
1244275 TATTTATCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 24 0.80
19 6 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATTATTTATTAATTAAA
Found at i:1245111 original size:15 final size:15
Alignment explanation
Indices: 1245091--1245160 Score: 97
Period size: 15 Copynumber: 4.7 Consensus size: 15
1245081 ATCCAGGTAT
1245091 CGGGTACCCGAATAC
1 CGGGTACCCGAATAC
1245106 CGGGTACCC-AATTAC
1 CGGGTACCCGAA-TAC
1245121 CGGGTACCCGAATAC
1 CGGGTACCCGAATAC
* * *
1245136 CAGGTATCCGATTAC
1 CGGGTACCCGAATAC
1245151 CGGGTACCCG
1 CGGGTACCCG
1245161 TAACATCCGG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
14 2 0.04
15 44 0.92
16 2 0.04
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (15 bp):
CGGGTACCCGAATAC
Found at i:1245127 original size:30 final size:30
Alignment explanation
Indices: 1245091--1245160 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
1245081 ATCCAGGTAT
*
1245091 CGGGTACCCGAATACCGGGTACCCAATTAC
1 CGGGTACCCGAATACCAGGTACCCAATTAC
* *
1245121 CGGGTACCCGAATACCAGGTATCCGATTAC
1 CGGGTACCCGAATACCAGGTACCCAATTAC
1245151 CGGGTACCCG
1 CGGGTACCCG
1245161 TAACATCCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (30 bp):
CGGGTACCCGAATACCAGGTACCCAATTAC
Found at i:1249022 original size:34 final size:34
Alignment explanation
Indices: 1248914--1249025 Score: 97
Period size: 34 Copynumber: 3.2 Consensus size: 34
1248904 TTTTTGGGCC
*
1248914 ACCCGACCCGAGAAGAAAGGGTCTTCCACCCGTG
1 ACCCGACCCGAGAAGAAAGGGTCCTCCACCCGTG
* * * *
1248948 ACCTGACCCGCCGAA-ATTAAGGTTTCACAT-GACCC--G
1 ACCCGACCCG-AGAAGA--AAGG-GTC-C-TCCACCCGTG
1248984 ACCCGACCCGAGAAGAAAGGGTCCTCCACCCGTG
1 ACCCGACCCGAGAAGAAAGGGTCCTCCACCCGTG
1249018 ACCCGACC
1 ACCCGACC
1249026 TGACCAACCC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
31 1 0.02
32 5 0.08
33 2 0.03
34 23 0.39
35 6 0.10
36 15 0.25
37 2 0.03
38 4 0.07
39 1 0.02
ACGTcount: A:0.27, C:0.38, G:0.23, T:0.12
Consensus pattern (34 bp):
ACCCGACCCGAGAAGAAAGGGTCCTCCACCCGTG
Found at i:1249616 original size:2 final size:2
Alignment explanation
Indices: 1249609--1249634 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1249599 TATGTTATTA
1249609 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
1249635 TCATCTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1249904 original size:17 final size:17
Alignment explanation
Indices: 1249871--1249920 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1249861 TAACCGACTC
*
1249871 AATAAAAATAAGAATTTA
1 AATAAAAATAA-TATTTA
*
1249889 ATTAAAAATAATATTTA
1 AATAAAAATAATATTTA
* *
1249906 AAAAAAAATTATATT
1 AATAAAAATAATATT
1249921 ATTATCGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AATAAAAATAATATTTA
Found at i:1250317 original size:48 final size:49
Alignment explanation
Indices: 1250243--1250341 Score: 123
Period size: 48 Copynumber: 2.0 Consensus size: 49
1250233 AATGAAAATC
* * *
1250243 TGAGTTTACAATTATAAAAAATAAAATA-ATTAAAAAAA-GCCACGTGTG
1 TGAGTTTACAATTATAAAAAAAAAAATATA-AAAAAAAACCCCACGTGTG
*
1250291 TGAGTTTAGAATTA-AAAAATAAAAAATATAAAAAAAAACCCCACGTGTG
1 TGAGTTTACAATTATAAAAA-AAAAAATATAAAAAAAAACCCCACGTGTG
1250340 TG
1 TG
1250342 TGGGTGTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
47 5 0.11
48 27 0.61
49 12 0.27
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (49 bp):
TGAGTTTACAATTATAAAAAAAAAAATATAAAAAAAAACCCCACGTGTG
Found at i:1250407 original size:20 final size:20
Alignment explanation
Indices: 1250351--1250488 Score: 131
Period size: 20 Copynumber: 6.8 Consensus size: 20
1250341 GTGGGTGTCT
1250351 TCTTCTTCTTCTTCTTGGTG
1 TCTTCTTCTTCTTCTTGGTG
* * *
1250371 TCTTGGTGTCTTGTTCTT-CT-
1 TCTT-CT-TCTTCTTCTTGGTG
* *
1250391 TCTTCTTGGTATCTTCTT-CT-
1 TCTTCTT-CT-TCTTCTTGGTG
*
1250411 TCTTCTTCTTCTTCTTGGTA
1 TCTTCTTCTTCTTCTTGGTG
1250431 TCTTCTTCTTCTTCTTGGTG
1 TCTTCTTCTTCTTCTTGGTG
1250451 TCTTCTTCTTCTTCTTGGTG
1 TCTTCTTCTTCTTCTTGGTG
*
1250471 TCTTGTTGTCTTCTTCTT
1 TCTT-CT-TCTTCTTCTT
1250489 CTTCTTCCTA
Statistics
Matches: 100, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
18 8 0.08
19 4 0.04
20 66 0.66
21 3 0.03
22 19 0.19
ACGTcount: A:0.01, C:0.24, G:0.14, T:0.61
Consensus pattern (20 bp):
TCTTCTTCTTCTTCTTGGTG
Found at i:1250514 original size:3 final size:3
Alignment explanation
Indices: 1250348--1250495 Score: 100
Period size: 3 Copynumber: 45.7 Consensus size: 3
1250338 TGTGTGGGTG
* * *
1250348 TCT TCT TCT TCT TCT TCT TGGT GTCT TGGT GTCT TGT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT T-CT -TCT T-CT -TCT TCT TCT TCT TCT TCT
* *
1250397 TGGT ATCT TCT TCT TCT TCT TCT TCT TCT TGGT ATCT TCT TCT TCT TCT
1 T-CT -TCT TCT TCT TCT TCT TCT TCT TCT T-CT -TCT TCT TCT TCT TCT
* * * *
1250446 TGGT GTCT TCT TCT TCT TCT TGGT GTCT TGT T-G TCT TCT TCT TCT TCT
1 T-CT -TCT TCT TCT TCT TCT T-CT -TCT TCT TCT TCT TCT TCT TCT TCT
1250494 TC
1 TC
1250496 CTAACAATAG
Statistics
Matches: 115, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
2 1 0.01
3 96 0.83
4 12 0.10
5 6 0.05
ACGTcount: A:0.01, C:0.25, G:0.13, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:1250605 original size:40 final size:40
Alignment explanation
Indices: 1250554--1250632 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
1250544 TTCAATAAAA
1250554 TAATAATATTTTAAAAATCATTGTTGAAAGAATTTCAAAC
1 TAATAATATTTTAAAAATCATTGTTGAAAGAATTTCAAAC
1250594 TAATAATATTTTAAAAATCATTGTTGAAAGAATTTCAAA
1 TAATAATATTTTAAAAATCATTGTTGAAAGAATTTCAAA
1250633 AATTTTCTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (40 bp):
TAATAATATTTTAAAAATCATTGTTGAAAGAATTTCAAAC
Found at i:1256304 original size:16 final size:16
Alignment explanation
Indices: 1256280--1256314 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1256270 GTTGTTAATC
1256280 AACGAACAGACGAGGA
1 AACGAACAGACGAGGA
*
1256296 AACGGACAGACGAGGA
1 AACGAACAGACGAGGA
1256312 AAC
1 AAC
1256315 AGTCACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.31, T:0.00
Consensus pattern (16 bp):
AACGAACAGACGAGGA
Found at i:1257232 original size:29 final size:30
Alignment explanation
Indices: 1257198--1257287 Score: 78
Period size: 29 Copynumber: 3.0 Consensus size: 30
1257188 CTATGATAGT
1257198 TATTCTAAATTAGTCCTTAAACTTTTAAAC
1 TATTCTAAATTAGTCCTTAAACTTTTAAAC
* * * **
1257228 -ATTCT-AATTCCA-TCCTCAAACTATGACTC
1 TATTCTAAATT--AGTCCTTAAACTTTTAAAC
*
1257257 TTATTCTAAATTAGTCCCTAAACTTTTAAAC
1 -TATTCTAAATTAGTCCTTAAACTTTTAAAC
1257288 CTTCCAATTG
Statistics
Matches: 43, Mismatches: 11, Indels: 11
0.66 0.17 0.17
Matches are distributed among these distances:
28 4 0.09
29 17 0.40
30 2 0.05
31 16 0.37
32 4 0.09
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (30 bp):
TATTCTAAATTAGTCCTTAAACTTTTAAAC
Found at i:1257279 original size:60 final size:60
Alignment explanation
Indices: 1257184--1257296 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
1257174 CCTATGTCCC
* * *
1257184 CAAACTATGATAGTTATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTCCATCCT
1 CAAACTATGATACTTATTCTAAATTAGTCCCTAAACTTTTAAACATTCCAATTCCATCCT
*
1257244 CAAACTATGACT-CTTATTCTAAATTAGTCCCTAAACTTTTAAACCTTCCAATT
1 CAAACTATGA-TACTTATTCTAAATTAGTCCCTAAACTTTTAAACATTCCAATT
1257297 GCATTCCTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 47 0.98
61 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (60 bp):
CAAACTATGATACTTATTCTAAATTAGTCCCTAAACTTTTAAACATTCCAATTCCATCCT
Found at i:1266444 original size:9 final size:9
Alignment explanation
Indices: 1266427--1266464 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
1266417 TGGCTGAAGC
1266427 TCCTCTTCT
1 TCCTCTTCT
*
1266436 TCGTCTTCT
1 TCCTCTTCT
*
1266445 TCCTCCTCT
1 TCCTCTTCT
1266454 TCCTCTTCT
1 TCCTCTTCT
1266463 TC
1 TC
1266465 TTCATATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.53
Consensus pattern (9 bp):
TCCTCTTCT
Found at i:1266496 original size:9 final size:9
Alignment explanation
Indices: 1266479--1266536 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
1266469 TATTCACCTC
*
1266479 CATCATCGT
1 CATCGTCGT
1266488 CATCGTCGT
1 CATCGTCGT
*
1266497 CATCATC-T
1 CATCGTCGT
1266505 --TCGTCGT
1 CATCGTCGT
* *
1266512 CGTCTTCGT
1 CATCGTCGT
*
1266521 CATCTTCGT
1 CATCGTCGT
1266530 CATCGTC
1 CATCGTC
1266537 TTCGTCCTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
6 4 0.10
7 1 0.03
8 1 0.03
9 34 0.85
ACGTcount: A:0.12, C:0.34, G:0.16, T:0.38
Consensus pattern (9 bp):
CATCGTCGT
Found at i:1266508 original size:12 final size:12
Alignment explanation
Indices: 1266487--1266549 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 12
1266477 TCCATCATCG
*
1266487 TCATCGTCGTCA
1 TCATCTTCGTCA
*
1266499 TCATCTTCGTCG
1 TCATCTTCGTCA
*
1266511 TCGTCTTCG---
1 TCATCTTCGTCA
1266520 TCATCTTCGTCA
1 TCATCTTCGTCA
* *
1266532 TCGTCTTCGTCC
1 TCATCTTCGTCA
1266544 TCATCT
1 TCATCT
1266550 CCACTTGCTC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
9 8 0.20
12 33 0.80
ACGTcount: A:0.10, C:0.35, G:0.14, T:0.41
Consensus pattern (12 bp):
TCATCTTCGTCA
Found at i:1266537 original size:21 final size:21
Alignment explanation
Indices: 1266479--1266542 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
1266469 TATTCACCTC
* * *
1266479 CATCATCGTCATCGTCGTCAT
1 CATCTTCGTCATCGTCTTCGT
*
1266500 CATCTTCGTCGTCGTCTTCGT
1 CATCTTCGTCATCGTCTTCGT
1266521 CATCTTCGTCATCGTCTTCGT
1 CATCTTCGTCATCGTCTTCGT
1266542 C
1 C
1266543 CTCATCTCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.11, C:0.34, G:0.16, T:0.39
Consensus pattern (21 bp):
CATCTTCGTCATCGTCTTCGT
Found at i:1268003 original size:30 final size:30
Alignment explanation
Indices: 1267960--1268044 Score: 134
Period size: 30 Copynumber: 2.8 Consensus size: 30
1267950 AATTTTGAAT
* *
1267960 AAAAATGAAAGTTTAGGTACTAAACGGACC
1 AAAACTGATAGTTTAGGTACTAAACGGACC
*
1267990 AAAACTGATAGTTTAGGTACTAAACGGATC
1 AAAACTGATAGTTTAGGTACTAAACGGACC
*
1268020 AAAACTGATAGTTTAAGTACTAAAC
1 AAAACTGATAGTTTAGGTACTAAAC
1268045 ATGTTAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.25
Consensus pattern (30 bp):
AAAACTGATAGTTTAGGTACTAAACGGACC
Found at i:1268589 original size:21 final size:20
Alignment explanation
Indices: 1268563--1268604 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1268553 AACATAGAAG
1268563 TCAAATTCGCAACACGGAATT
1 TCAAATTCGCAACAC-GAATT
* *
1268584 TCAAATTTGCAACGCGAATT
1 TCAAATTCGCAACACGAATT
1268604 T
1 T
1268605 ATTTTTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (20 bp):
TCAAATTCGCAACACGAATT
Found at i:1268670 original size:40 final size:40
Alignment explanation
Indices: 1268626--1268717 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
1268616 ATAAGTTTCC
* *
1268626 TTTTCGCAACAAGATTTTCTAAATCGCAACACGAATTTTG
1 TTTTCGCAACAAGATTTTCGAAATCGCAACACGAATTTTA
* ** *
1268666 TTTTC-TATACTCGATTTTCGAATTCGCAACACGAATTTTA
1 TTTTCGCA-ACAAGATTTTCGAAATCGCAACACGAATTTTA
*
1268706 ATTTCGCAACAA
1 TTTTCGCAACAA
1268718 CTTTTATTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
39 1 0.03
40 38 0.95
41 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (40 bp):
TTTTCGCAACAAGATTTTCGAAATCGCAACACGAATTTTA
Found at i:1268713 original size:20 final size:19
Alignment explanation
Indices: 1268688--1268737 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
1268678 GATTTTCGAA
1268688 TTCGCAACACGAATTTTAAT
1 TTCGCAACAC-AATTTTAAT
* *
1268708 TTCGCAACA-ACTTTTATT
1 TTCGCAACACAATTTTAAT
1268726 TTCGCAACACAA
1 TTCGCAACACAA
1268738 ATATTTTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 16 0.62
19 1 0.04
20 9 0.35
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (19 bp):
TTCGCAACACAATTTTAAT
Found at i:1268891 original size:14 final size:15
Alignment explanation
Indices: 1268872--1268909 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1268862 TCCCCATCTC
1268872 TAATTTTTTT-TAGA
1 TAATTTTTTTATAGA
*
1268886 TAATTTTATTTATATA
1 TAATTTT-TTTATAGA
1268902 TAATTTTT
1 TAATTTTT
1268910 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTATAGA
Found at i:1270173 original size:30 final size:30
Alignment explanation
Indices: 1269964--1270156 Score: 350
Period size: 30 Copynumber: 6.4 Consensus size: 30
1269954 TTCGAAGGAC
*
1269964 CTATCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1269994 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1270024 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1270054 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1270084 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1270114 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1270144 CTATCCATAGGTC
1 CTATCCAGAGGTC
1270157 CCGAAGAACC
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 157 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1270173 original size:90 final size:90
Alignment explanation
Indices: 1269964--1270179 Score: 333
Period size: 90 Copynumber: 2.4 Consensus size: 90
1269954 TTCGAAGGAC
* * * *
1269964 CTATCCAGAGGTCATAAAGATCTTCGGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATC
1270029 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* * *
1270054 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATC
1270119 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* * *
1270144 CTATCCATAGGTCCCGAAGAACCTAGGTAAACTATC
1 CTATCCAGAGGTCACAAAGAACCTAGGT-AACTATC
1270180 TATATGTTCC
Statistics
Matches: 118, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
90 111 0.94
91 7 0.06
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (90 bp):
CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCATAAAGATCCTCGGTAA
Found at i:1270773 original size:2 final size:2
Alignment explanation
Indices: 1270766--1270852 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
1270756 TACACAACTC
1270766 AT AT AT AT AT 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 AT AT AT AT AT
1270808 AT AT AT AT AT 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 AT AT AT AT AT
1270850 AT A
1 AT A
1270853 CTGTAACATG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1271393 original size:19 final size:20
Alignment explanation
Indices: 1271356--1271393 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1271346 TTTTTCATTA
*
1271356 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1271376 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1271394 TCTAGCATTC
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:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1271445 original size:21 final size:21
Alignment explanation
Indices: 1271421--1271463 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1271411 TCATATTCGT
* *
1271421 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
1271442 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
1271463 T
1 T
1271464 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:1275002 original size:30 final size:30
Alignment explanation
Indices: 1274801--1274985 Score: 316
Period size: 30 Copynumber: 6.2 Consensus size: 30
1274791 ACCTATTCAT
* *
1274801 AGGTCATAAAGATCTTCGGTAACTATCCAA
1 AGGTCATAAAGATCCTCGGTAACTATCCAG
1274831 AGGTCATAAAGATCCTCGGTAACTATCCAG
1 AGGTCATAAAGATCCTCGGTAACTATCCAG
1274861 AGGTCATAAAGATCCTCGGTAACTATCCAG
1 AGGTCATAAAGATCCTCGGTAACTATCCAG
* * *
1274891 AGGTTATAAATATCCTCGGTAACTATCCAA
1 AGGTCATAAAGATCCTCGGTAACTATCCAG
1274921 AGGTCATAAAGATCCTCGGTAACTATCCAG
1 AGGTCATAAAGATCCTCGGTAACTATCCAG
*
1274951 AGGTCATAAAGATCCTCGGTAACTATCCAT
1 AGGTCATAAAGATCCTCGGTAACTATCCAG
1274981 AGGTC
1 AGGTC
1274986 CCGAAGAACC
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 146 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (30 bp):
AGGTCATAAAGATCCTCGGTAACTATCCAG
Found at i:1275002 original size:90 final size:90
Alignment explanation
Indices: 1274818--1275010 Score: 305
Period size: 90 Copynumber: 2.1 Consensus size: 90
1274808 AAAGATCTTC
1274818 GGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 GGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * *
1274883 CTATCCAGAGGTTATAAATATCCTC
66 CTATCCAGAGGTCACAAAGAACCTA
1274908 GGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 GGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * *
1274973 CTATCCATAGGTCCCGAAGAACCTA
66 CTATCCAGAGGTCACAAAGAACCTA
1274998 GGTAAACTATCCA
1 GGT-AACTATCCA
1275011 TATGTTCCTT
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 85 0.90
91 9 0.10
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (90 bp):
GGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
CTATCCAGAGGTCACAAAGAACCTA
Found at i:1275009 original size:31 final size:31
Alignment explanation
Indices: 1274971--1275063 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
1274961 GATCCTCGGT
* *
1274971 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
1275002 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* *
1275033 TACTATCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
1275064 GTTCTTTGAC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 1 0.02
31 50 0.98
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:1275246 original size:4 final size:4
Alignment explanation
Indices: 1275237--1276148 Score: 1734
Period size: 4 Copynumber: 230.2 Consensus size: 4
1275227 ATATAACCCT
1275237 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275285 TACA TACA TACA TACA TACA TACA -ACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
1275332 TACA TACA TACA TACA TACA GACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275380 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275428 -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275475 TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275521 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275569 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275617 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275665 TACA TACA TACA T--A TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275711 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275759 TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
1275805 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA AACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275853 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
1275901 TACA TACA GACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275949 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1275997 TACA TACA TACA TACA TACA TACA TACA TA-A TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1276044 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1276092 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1276140 TACA TACA T
1 TACA TACA T
1276149 GTCATCATTT
Statistics
Matches: 893, Mismatches: 6, Indels: 18
0.97 0.01 0.02
Matches are distributed among these distances:
2 6 0.01
3 9 0.01
4 878 0.98
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:1277058 original size:19 final size:20
Alignment explanation
Indices: 1277021--1277058 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1277011 TTTTTCATTA
*
1277021 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1277041 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1277059 TCTAGCATTC
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:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1278208 original size:24 final size:24
Alignment explanation
Indices: 1278157--1278210 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1278147 GTATTCGAAA
*
1278157 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCAGGAC
* *
1278181 TTTGATCTTGGTCAATACTAGGAT
1 TTTGATCTTGGTCAATACCAGGAC
1278205 TTTGAT
1 TTTGAT
1278211 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGGAC
Found at i:1280151 original size:30 final size:31
Alignment explanation
Indices: 1280095--1280155 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1280085 CAATTTAAGG
1280095 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1280126 CAAAATGGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1280156 TTCAAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:1280326 original size:20 final size:20
Alignment explanation
Indices: 1280301--1280368 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
1280291 TGAATCGATG
*
1280301 TCGATGCATCCTTATGTGCA
1 TCGATGCATCCTGATGTGCA
* *
1280321 TCGATGCATGCTGCTGTGCA
1 TCGATGCATCCTGATGTGCA
* *
1280341 TCGATGCATCCTGCTATGCA
1 TCGATGCATCCTGATGTGCA
*
1280361 TCCATGCA
1 TCGATGCA
1280369 CCAAGGCTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.31
Consensus pattern (20 bp):
TCGATGCATCCTGATGTGCA
Found at i:1281456 original size:18 final size:18
Alignment explanation
Indices: 1281430--1281465 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1281420 AAGAAAAAGG
* *
1281430 AAATTAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1281448 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1281466 CAACTGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1282367 original size:23 final size:23
Alignment explanation
Indices: 1282336--1282380 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1282326 CACCGCAGCT
*
1282336 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1282359 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1282381 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1282570 original size:103 final size:103
Alignment explanation
Indices: 1282397--1282614 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1282387 TAATGTCCAT
* * *
1282397 AAGGACAACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1282462 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1282500 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1282565 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1282603 AAGGACCACATA
1 AAGGACCACATA
1282615 GACCCTCAAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1285091 original size:2 final size:2
Alignment explanation
Indices: 1285084--1285139 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1285074 CCTTTTCCTT
1285084 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1285125 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1285140 TCATATCATG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1287508 original size:23 final size:23
Alignment explanation
Indices: 1287477--1287545 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1287467 CACCGCAGCT
*
1287477 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1287500 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
1287523 CATAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1287546 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1287810 original size:103 final size:103
Alignment explanation
Indices: 1287561--1287883 Score: 547
Period size: 103 Copynumber: 3.1 Consensus size: 103
1287551 TAATGTCCAT
* * * * *
1287561 AAGGACTACATAACATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1287626 GACTTCACACATGTTCCAAAGAATATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAG-A-ATACATATATGTCCCG
*
1287666 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1287731 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1287769 AAGGACCACATATCATTCCTTAAGAATTATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1287834 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1287872 AAGGACCACATA
1 AAGGACCACATA
1287884 GACCCTCAAC
Statistics
Matches: 207, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
103 127 0.61
104 1 0.00
105 79 0.38
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1291791 original size:21 final size:21
Alignment explanation
Indices: 1291767--1291864 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
1291757 GTGAATCGGG
* *
1291767 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1291788 CTCTTGAACAATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1291809 CTCTTGAACGATGAGAGTGGC
1 CTCTTGAACGATGAGAGGGGC
* *
1291830 CTCTTAAACGAT-AGGAGGAGC
1 CTCTTGAACGATGA-GAGGGGC
1291851 CTCTTGAACGATGA
1 CTCTTGAACGATGA
1291865 CAGGTGAATC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
20 1 0.02
21 64 0.97
22 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1292236 original size:21 final size:20
Alignment explanation
Indices: 1292181--1292238 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
1292171 ATAAAGTAGA
1292181 TACCTCACCACGTAAAACAC
1 TACCTCACCACGTAAAACAC
* ** * *
1292201 CATTGTCATCGCGTAAAACATC
1 TA-CCTCACCACGTAAAACA-C
1292223 TACCTCACCACGTAAA
1 TACCTCACCACGTAAA
1292239 GACCGTACCT
Statistics
Matches: 26, Mismatches: 10, Indels: 3
0.67 0.26 0.08
Matches are distributed among these distances:
20 1 0.04
21 23 0.88
22 2 0.08
ACGTcount: A:0.36, C:0.34, G:0.09, T:0.21
Consensus pattern (20 bp):
TACCTCACCACGTAAAACAC
Found at i:1292517 original size:42 final size:42
Alignment explanation
Indices: 1292436--1292534 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
1292426 GTGATGGAAT
* * *
1292436 AGGTGATGGCTCTCGTTGTAGAGGTATATAATCGGCTCGATC
1 AGGTGATGGCTCTCGTTGTAGAGCTATAGAATCGACTCGATC
* * *
1292478 AGGTGATGGCTCTGCG-TGTCGAGCTGTAGAATTGACTCGATC
1 AGGTGATGGCTCT-CGTTGTAGAGCTATAGAATCGACTCGATC
* *
1292520 AAGTGATGACTCTCG
1 AGGTGATGGCTCTCG
1292535 AAGTGGGGGG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.04
42 44 0.92
43 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.29
Consensus pattern (42 bp):
AGGTGATGGCTCTCGTTGTAGAGCTATAGAATCGACTCGATC
Found at i:1294011 original size:20 final size:20
Alignment explanation
Indices: 1293988--1294026 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1293978 TTGAAACTTA
1293988 AATTCGCAACACGAAAATGT
1 AATTCGCAACACGAAAATGT
*
1294008 AATTCGCAACGCGAAAATG
1 AATTCGCAACACGAAAATG
1294027 AAAATCGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
AATTCGCAACACGAAAATGT
Found at i:1294034 original size:20 final size:20
Alignment explanation
Indices: 1293991--1294034 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1293981 AAACTTAAAT
* *
1293991 TCGCAACACGAAAATGTAAT
1 TCGCAACACGAAAATGAAAA
*
1294011 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
1294031 TCGC
1 TCGC
1294035 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:1294106 original size:20 final size:20
Alignment explanation
Indices: 1294041--1294099 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
1294031 TCGCGTTGCG
*
1294041 ATTTTCGTGTTGCGACTTTC
1 ATTTTCGTGTTGCGAATTTC
*
1294061 ATTTTCATGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
1294081 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
1294100 AAGTTTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Done.