Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 6 of 17
Found at i:1068600 original size:125 final size:129
Alignment explanation
Indices: 1068290--1068608 Score: 318
Period size: 130 Copynumber: 2.5 Consensus size: 129
1068280 GTACATTGTT
* *
1068290 AATTTACCTATTACTTTAAAGTAATAGGT-TTCGAAATTATAAG-AGTTGATAC-TTAT-ATGAC
1 AATTTACCTATTACTTTAAAGTAATAAGTGTTCGAAATTATAAGTA-TCGATACTTTATAATG--
* * *
1068351 TGTATCGATACTTGTACATTCACGCCTATTTTCATTATACCGGTAGAAACGTTTATCGTGTCCAT
63 TGTATCAATACTTGTACATTCACGCCTATTATCATTATA-CAGTAG-AACGTTTATCGTGTCCAT
* *
1068416 TGTT
126 TATA
* * ** * *
1068420 AATTTACCCATTACTTTAAAGCAAT-AG-GTTCGAAATTGCACGTATCGATATTTTATACATGTG
1 AATTTACCTATTACTTTAAAGTAATAAGTGTTCGAAATTATAAGTATCGATACTTTATA-ATGTG
* * * * *
1068483 TATCAATACTTG-ATATTTACGCCTATTATCATTAT-CAGTAG-ACTTTTA-CGTTTTCATTATA
65 TATCAATACTTGTACATTCACGCCTATTATCATTATACAGTAGAACGTTTATCGTGTCCATTATA
* *
1068544 AATTAACCTATTACTTTATAGTAATAAGTGTT-GAAATTATAAGTATCGATACTTTATATATGTG
1 AATTTACCTATTACTTTAAAGTAATAAGTGTTCGAAATTATAAGTATCGATACTTTATA-ATGTG
1068608 T
65 T
1068609 CTCGATACAT
Statistics
Matches: 155, Mismatches: 27, Indels: 19
0.77 0.13 0.09
Matches are distributed among these distances:
124 30 0.19
125 36 0.23
126 3 0.02
127 5 0.03
129 37 0.24
130 41 0.26
132 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (129 bp):
AATTTACCTATTACTTTAAAGTAATAAGTGTTCGAAATTATAAGTATCGATACTTTATAATGTGT
ATCAATACTTGTACATTCACGCCTATTATCATTATACAGTAGAACGTTTATCGTGTCCATTATA
Found at i:1068900 original size:197 final size:196
Alignment explanation
Indices: 1068488--1069017 Score: 515
Period size: 197 Copynumber: 2.7 Consensus size: 196
1068478 ATGTGTATCA
* * * * ** * *
1068488 ATACTTGATATTTACGCCTATTATCAT--TATCAGTAGACTTTTA-CGTTTTCATTATAAATTAA
1 ATACTTTATATTTACGCCTATTATCATAAAACCAATAGACTTTTACCGTTGACATTGTAAATTTA
* * * ** * * * * * ** *
1068550 CCTATTACTTTATAGTAATAAGTGTT-GAAATTATAAGTATCGATACTTTATATATGTGTCTCGA
66 CATATAACTTTAAAGTAATCGGT-TTCAAAATT-TCACTATCAATAATTTATACGTGTGTATCGA
* * *
1068614 TACATTT-TGCGTGCAAAATTTTTGAGAAGATACTGGAATAAAGTACGATACCTATATAGATAGT
129 TAC-TTTGTGCGTGCAAAATTATTGAGAAGATACTAGAATAAAGTACGATACCTATATAGAAAGT
*
1068678 ATCG
193 ATAG
**
1068682 ATACTTTATATTTACGCCTATTATCA-AAATACCAATAGGTTTTTACCGTTGACATTGTAAATTT
1 ATACTTTATATTTACGCCTATTATCATAAA-ACCAATAGACTTTTACCGTTGACATTGTAAATTT
1068746 ACATATAACTTTAAAGTAATCGGTTTCAAAATTCTGCA-TATCAATAATTTATACGTGTGTATCG
65 ACATATAACTTTAAAGTAATCGGTTTCAAAATT-T-CACTATCAATAATTTATACGTGTGTATCG
* *
1068810 ATACTTTGTGCGTGC-AAATTATTGAGAAGCATATTAGACTAAAAGTATCGATACCTATA-A-AA
128 ATACTTTGTGCGTGCAAAATTATTGAGAAG-ATACTAGAAT-AAAGTA-CGATACCTATATAGAA
*
1068872 AGTATAT
190 AGTATAG
* * * ** * *
1068879 ATACTTGT-TGTTTATGCCTATTATCATTAAACCGGTAGACTTTTATCGTTTACATTGTAAATTT
1 ATACTT-TATATTTACGCCTATTATCATAAAACCAATAGACTTTTACCGTTGACATTGTAAATTT
* * * *
1068943 ACCTATAACTTTAAAGTAATCGGTTTCGAAATTTCACTTATCGATACTTTATACGTGTGTATCGA
65 ACATATAACTTTAAAGTAATCGGTTTCAAAATTTCAC-TATCAATAATTTATACGTGTGTATCGA
1069008 TACTTTGTGC
129 TACTTTGTGC
1069018 ATGTGTATCG
Statistics
Matches: 279, Mismatches: 43, Indels: 25
0.80 0.12 0.07
Matches are distributed among these distances:
194 25 0.09
195 2 0.01
196 30 0.11
197 200 0.72
198 11 0.04
199 11 0.04
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (196 bp):
ATACTTTATATTTACGCCTATTATCATAAAACCAATAGACTTTTACCGTTGACATTGTAAATTTA
CATATAACTTTAAAGTAATCGGTTTCAAAATTTCACTATCAATAATTTATACGTGTGTATCGATA
CTTTGTGCGTGCAAAATTATTGAGAAGATACTAGAATAAAGTACGATACCTATATAGAAAGTATA
G
Found at i:1069035 original size:21 final size:21
Alignment explanation
Indices: 1068981--1069038 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1068971 AAATTTCACT
* * *
1068981 TATCGATACTTTATACGTGTG
1 TATCGATACTTTGTGCATGTG
1069002 TATCGATACTTTGTGCATGTG
1 TATCGATACTTTGTGCATGTG
1069023 TATCGATACTTTGTGC
1 TATCGATACTTTGTGC
1069039 TTGCAAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.43
Consensus pattern (21 bp):
TATCGATACTTTGTGCATGTG
Found at i:1069214 original size:218 final size:219
Alignment explanation
Indices: 1068784--1069502 Score: 1069
Period size: 218 Copynumber: 3.3 Consensus size: 219
1068774 AAATTCTGCA
* * * * * *
1068784 TATCAATAATTTATACGTGTGTATCGATACTTTGTGCGTGCAAATTATTGAGAAGCATATTAGAC
1 TATCGATACTTTATACATGTGTATCGATACTTTGTGCATGCAAATTGTTGAGAAGCATACTAGAC
** * *
1068849 TAAAAGTATCGATACCTAT--AAAAAGTATATATACTTGTTGTTTATGCCTATTATCATTAAACC
66 TAAAAGTATCGATACCTATACAAAAAGTATCGATACTTGATGTTTACGCCTATTATCATTAAACC
1068912 GGTAGACTTTTA-TCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATT
131 GGTAGACTTTTACT-GTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATT
* * *
1068976 TC-ACTTATCGATACTTTATACGTGTG
195 CCGA-TTATCTATA-TTTATACATGTG
* * * * *
1069002 TATCGATACTTTGTGCATGTGTATCGATACTTTGTGCTTGCAAATTGTTGAGAAGCACACTGGAC
1 TATCGATACTTTATACATGTGTATCGATACTTTGTGCATGCAAATTGTTGAGAAGCATACTAGAC
*
1069067 TAAAAGTATCGATACCTATACAAAAAGTTTCGATACTTGATGTTTACGCCTATTATCATTAAACC
66 TAAAAGTATCGATACCTATACAAAAAGTATCGATACTTGATGTTTACGCCTATTATCATTAAACC
*
1069132 GGTAGACTTTTACTGTTTACATTATAAATTTACCTATAAC-TTAAAGTAATCGGTTTCG-AATTC
131 GGTAGACTTTTACTGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATTC
*
1069195 CGTTTATCTATATTTTATACATGTG
196 CGATTATCTATA-TTTATACATGTG
*
1069220 TATCGATACTTTATACATGTGTATCGATACTTTGTGCATGCAAATTGTTGAGAAGCATACTGGAC
1 TATCGATACTTTATACATGTGTATCGATACTTTGTGCATGCAAATTGTTGAGAAGCATACTAGAC
*
1069285 TAAAAGTATCGATACCTATACAAAAAGTATCGATACTTGATGTTTACGCCTATTATCATTAAACT
66 TAAAAGTATCGATACCTATACAAAAAGTATCGATACTTGATGTTTACGCCTATTATCATTAAACC
** *
1069350 AATAGACTTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATTC
131 GGTAGACTTTTACTGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATTC
* *
1069415 CGAATATCTATACTTA-ACATGTG
196 CGATTATCTATATTTATACATGTG
* *
1069438 TATTGATACTTTATACATATGTAT-GATACTTT-TGCATGCAAATTGTTGAGAAGCATACTAGAC
1 TATCGATACTTTATACATGTGTATCGATACTTTGTGCATGCAAATTGTTGAGAAGCATACTAGAC
1069501 TA
66 TA
1069503 TCGATACTTG
Statistics
Matches: 458, Mismatches: 37, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
216 32 0.07
217 8 0.02
218 287 0.63
219 39 0.09
220 91 0.20
221 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (219 bp):
TATCGATACTTTATACATGTGTATCGATACTTTGTGCATGCAAATTGTTGAGAAGCATACTAGAC
TAAAAGTATCGATACCTATACAAAAAGTATCGATACTTGATGTTTACGCCTATTATCATTAAACC
GGTAGACTTTTACTGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATTC
CGATTATCTATATTTATACATGTG
Found at i:1069259 original size:21 final size:21
Alignment explanation
Indices: 1069199--1069252 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1069189 GAATTCCGTT
* *
1069199 TATCTATATTTTATACATGTG
1 TATCGATACTTTATACATGTG
1069220 TATCGATACTTTATACATGTG
1 TATCGATACTTTATACATGTG
1069241 TATCGATACTTT
1 TATCGATACTTT
1069253 GTGCATGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (21 bp):
TATCGATACTTTATACATGTG
Found at i:1069466 original size:20 final size:21
Alignment explanation
Indices: 1069424--1069469 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1069414 CCGAATATCT
*
1069424 ATAC-TTA-ACATGTGTATTG
1 ATACTTTATACATATGTATTG
1069443 ATACTTTATACATATGTA-TG
1 ATACTTTATACATATGTATTG
1069463 ATACTTT
1 ATACTTT
1069470 TGCATGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 12 0.50
21 8 0.33
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (21 bp):
ATACTTTATACATATGTATTG
Found at i:1070108 original size:21 final size:20
Alignment explanation
Indices: 1070075--1070113 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1070065 GCATAGTGAA
1070075 ATAAAAGTATCGATACTTAT
1 ATAAAAGTATCGATACTTAT
*
1070095 ATAATAAGTTTCGATACTT
1 ATAA-AAGTATCGATACTT
1070114 TATGTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (20 bp):
ATAAAAGTATCGATACTTAT
Found at i:1070299 original size:20 final size:22
Alignment explanation
Indices: 1070276--1070319 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1070266 GCATACTGGA
*
1070276 ATAA-AAGTATTGATA-CTTAT
1 ATAATAAGTATCGATACCTTAT
1070296 ATAATAAGTATCGATACCTTAT
1 ATAATAAGTATCGATACCTTAT
1070318 AT
1 AT
1070320 TTACGCCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 10 0.48
22 7 0.33
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (22 bp):
ATAATAAGTATCGATACCTTAT
Found at i:1070312 original size:201 final size:199
Alignment explanation
Indices: 1069501--1070422 Score: 1066
Period size: 201 Copynumber: 4.6 Consensus size: 199
1069491 CATACTAGAC
* * * *
1069501 TATCGATACTTGATGTTTACGCCTATTATAATTAAACTGGTAGA-TTTTACCGTTTACATTATAA
1 TATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGTAGATTTTTACCGTTTACATTGTAA
* * * *
1069565 ATTTACTTATTATTTTATAGTAATAGGTTTCAAAAATTACAAGTATCAATACTTTATACATGTGT
66 ATTTACCTATTACTTTAAAGTAATAGGTTTC-AAAATTATAAGTATCAATACTTTATACA--TGT
** * * * * *
1069630 ATCGATTTTTTTTTTCGTGCAAATTGTTTGAGATGCATGCTGGAATAAAAATATCGATACTTATA
128 ATCGATACTTTTTTGCATGCAAATTATTTGAGATGCATACTGGAATAAAAGTATCGATACTTATA
*
1069695 GAATAAG
193 TAATAAG
* * * *
1069702 TATCGATAGATACTTTATGTTTACACATATTATCATTAAACTGGTAGATTTTTACCATTTACATT
1 TATC----GATACTTTATGTTTACGCCTATTATCATTAAACCGGTAGATTTTTACCGTTTACATT
* * * ** * * *
1069767 GT-AATTTACGTATTACTTTATAGTAATAGGTTTCAAAATTACAAGTATTGATAATGTGTACATG
62 GTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCAATACTTTATACATG
* * * *
1069831 TATATCGATAC-TTTTTGCGTGCAAAATATTTGAGAAGCATACTGGAATAAAAGTATAGATA-TC
127 --TATCGATACTTTTTTGCATGCAAATTATTTGAGATGCATACTGGAATAAAAGTATCGATACT-
* *
1069894 TATACAAAAATG
189 TATATAATAA-G
* * *
1069906 TATCGATACTTTATGTTTACGCCTATTATCATTAAAACGATAGATTTTTACCGTTTATATTGTAA
1 TATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGTAGATTTTTACCGTTTACATTGTAA
* * * * * * **
1069971 ATTTACCTATTACTTTAAAGAAATTGGTTT-GAAAGTCTAAGTATC-ATACTTTACATGTGTATC
66 ATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCAATACTTTATACATGTATC
* * * * *
1070034 GATACTTTTTTGCATGAAAATTGTTTGAAATGCATAGTGAAATAAAAGTATCGATACTTATATAA
131 GATACTTTTTTGCATGCAAATTATTTGAGATGCATACTGGAATAAAAGTATCGATACTTATATAA
1070099 TAAG
196 TAAG
* * * **
1070103 TTTCGATACTTTATGTTTATGCCTATTATCATTAAACCGGTAGATTCTTATTGTTTACATTGTAA
1 TATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGTAGATTTTTACCGTTTACATTGTAA
* *
1070168 ATTTACCTATTACTTTAAAGAAATAAGTTTCAAAATTATAAGTATCAATACTTGTTATACATGTA
66 ATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCAATAC-T-TTATACATGTA
* *
1070233 TCGATACGTTTTTGCATGCAAATTATTTGAGATGCATACTGGAATAAAAGTATTGATACTTATAT
129 TCGATACTTTTTTGCATGCAAATTATTTGAGATGCATACTGGAATAAAAGTATCGATACTTATAT
1070298 AATAAG
194 AATAAG
* * * *
1070304 TATCGATACCTTATATTTACGCCTATTATCATTAAACCGGCATATTTTTACCGTTTACATTGTAA
1 TATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGTAGATTTTTACCGTTTACATTGTAA
* * * *
1070369 ATTTACATATTACTTTAAAGTAATACGTTTAAAAATTCTAAGTATCGAA-ACTTT
66 ATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATC-AATACTTT
1070423 GTTGCCGAAA
Statistics
Matches: 610, Mismatches: 94, Indels: 36
0.82 0.13 0.05
Matches are distributed among these distances:
197 95 0.16
198 61 0.10
199 15 0.02
200 64 0.10
201 202 0.33
202 5 0.01
203 51 0.08
204 35 0.06
205 66 0.11
206 16 0.03
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (199 bp):
TATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGTAGATTTTTACCGTTTACATTGTAA
ATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCAATACTTTATACATGTATC
GATACTTTTTTGCATGCAAATTATTTGAGATGCATACTGGAATAAAAGTATCGATACTTATATAA
TAAG
Found at i:1070325 original size:398 final size:402
Alignment explanation
Indices: 1069501--1070422 Score: 1120
Period size: 398 Copynumber: 2.3 Consensus size: 402
1069491 CATACTAGAC
* *
1069501 TATCGATA-CTTGATGTTTACGCCTATTATAATT-AAACTGGTAGA-TTTTACCGTTTACATTAT
1 TATCGATACCTT-ATGTTTACGCCTATTATCATTAAAAC-GGTAGATTTTTACCGTTTACATTGT
* * * *
1069563 AAATTTACTTATTATTTTATAGTAATAGGTTTCAAAAATTACAAGTATCAATACTTTATACATGT
64 AAATTTACATATTACTTTAAAGAAATAGGTTTCAAAAATTA-AAGTATCAATACTTTATACATGT
** * * * * *
1069628 GTATCGATTTTTTTTTTCGTGCAAATTGTTTGAGATGCATGCTGGAATAAAAATATCGATACTTA
128 GTATCGATACTTTTTTGCATGAAAATTGTTTGAAATGCATGCTGAAATAAAAATATCGATACTTA
* *
1069693 TAGAATAAGTATCGATAGATACTTTATGTTTACACATATTATCATTAAACTGGTAGATTTTTACC
193 TAGAATAAGTAT--ATAGATACTTTATGTTTACACATATTATCATTAAACCGGTAGATTCTTACC
* * * * **
1069758 ATTTACATTGTAATTTACGTATTACTTTATAGTAATAGGTTTCAAAATTACAAGTATTGATAATG
256 ATTTACATTGTAATTTACCTATTACTTTAAAGAAATAAGTTTCAAAATTACAAGTATCAATAATG
* *
1069823 TGTACATGTATATCGATACTTTTTGCGTGCAAAATATTTGAGAAGCATACTGGAATAAAAGTATA
321 TATACATG-ATATCGATACTTTTTGCATGCAAAATATTTGAGAAGCATACTGGAATAAAAGTATA
1069888 GATATCTATACAAAAATG
385 GATATCTATACAAAAATG
* * *
1069906 TATCGATACTTTATGTTTACGCCTATTATCATTAAAACGATAGATTTTTACCGTTTATATTGTAA
1 TATCGATACCTTATGTTTACGCCTATTATCATTAAAACGGTAGATTTTTACCGTTTACATTGTAA
* * * *
1069971 ATTTACCTATTACTTTAAAGAAATTGGTTT-GAAAGTCT-AAGTATC-ATAC-TT-TACATGTGT
66 ATTTACATATTACTTTAAAGAAATAGGTTTCAAAAAT-TAAAGTATCAATACTTTATACATGTGT
*
1070031 ATCGATACTTTTTTGCATGAAAATTGTTTGAAATGCATAG-TGAAATAAAAGTATCGATACTTAT
130 ATCGATACTTTTTTGCATGAAAATTGTTTGAAATGCAT-GCTGAAATAAAAATATCGATACTTAT
* * ** * ***
1070095 ATAATAAGT-T-TCGATACTTTATGTTTATGCCTATTATCATTAAACCGGTAGATTCTTATTGTT
194 AGAATAAGTATATAGATACTTTATGTTTACACATATTATCATTAAACCGGTAGATTCTTACCATT
* *
1070158 TACATTGTAAATTTACCTATTACTTTAAAGAAATAAGTTTCAAAATTATAAGTATCAATACTTGT
259 TACATTGT-AATTTACCTATTACTTTAAAGAAATAAGTTTCAAAATTACAAGTATCAATA-ATG-
* * *
1070223 TATACATG-TATCGATACGTTTTTGCATGCAAATTATTTGAGATGCATACTGGAATAAAAGTATT
321 TATACATGATATCGATAC-TTTTTGCATGCAAAATATTTGAGAAGCATACTGGAATAAAAGTATA
* *
1070287 GATA-CTTATATAATAA-G
385 GATATC-TATACAAAAATG
* * * *
1070304 TATCGATACCTTATATTTACGCCTATTATCATTAAACCGGCATATTTTTACCGTTTACATTGTAA
1 TATCGATACCTTATGTTTACGCCTATTATCATTAAAACGGTAGATTTTTACCGTTTACATTGTAA
* * *
1070369 ATTTACATATTACTTTAAAGTAATACGTTT-AAAAATTCTAAGTATCGAA-ACTTT
66 ATTTACATATTACTTTAAAGAAATAGGTTTCAAAAATT-AAAGTATC-AATACTTT
1070423 GTTGCCGAAA
Statistics
Matches: 444, Mismatches: 58, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
397 53 0.12
398 143 0.32
399 63 0.14
400 10 0.02
401 74 0.17
402 3 0.01
403 4 0.01
404 7 0.02
405 37 0.08
406 50 0.11
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (402 bp):
TATCGATACCTTATGTTTACGCCTATTATCATTAAAACGGTAGATTTTTACCGTTTACATTGTAA
ATTTACATATTACTTTAAAGAAATAGGTTTCAAAAATTAAAGTATCAATACTTTATACATGTGTA
TCGATACTTTTTTGCATGAAAATTGTTTGAAATGCATGCTGAAATAAAAATATCGATACTTATAG
AATAAGTATATAGATACTTTATGTTTACACATATTATCATTAAACCGGTAGATTCTTACCATTTA
CATTGTAATTTACCTATTACTTTAAAGAAATAAGTTTCAAAATTACAAGTATCAATAATGTATAC
ATGATATCGATACTTTTTGCATGCAAAATATTTGAGAAGCATACTGGAATAAAAGTATAGATATC
TATACAAAAATG
Found at i:1071694 original size:20 final size:21
Alignment explanation
Indices: 1071671--1071710 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1071661 TGCATACTGT
1071671 TATAA-AAGTATCGATACTTA
1 TATAATAAGTATCGATACTTA
1071691 TATAATAAGTATCGATACTT
1 TATAATAAGTATCGATACTT
1071711 TATGTTTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
TATAATAAGTATCGATACTTA
Found at i:1071919 original size:202 final size:201
Alignment explanation
Indices: 1071426--1072233 Score: 1036
Period size: 201 Copynumber: 4.0 Consensus size: 201
1071416 GAAATTATAA
* ** * * *
1071426 GTATTGATACTTTTTGCGTGCAAATTGTTTGTGATGCATATTAGAATACAAGTATCGATACTTAT
1 GTATCGATACTTTTTGCGTGCAAATTGTTTAAGATGCATACTGGAATAAAAGTATCGATACTTAT
* * * *
1071491 ATAATAAGTATCAATACTTGATGTTTATGCCTATTATCATTAAACCGATAGATTTTTACCGTTTA
66 ATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTCAACCGATAGATTTTTACCGTTT-
* *
1071556 T-ATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATTGATACTTG-T
130 TCATTGTAAATTTACCTATTACTTTAAAGAAATAGGTTTCGAAATTACAAGTATTGATACTTGTT
1071619 TATATGT
195 TATATGT
* * **
1071626 GTATCGATATTTTTTTACGTGCAAATTGTTTAAGATGCATACTGTTATAAAAGTATCGATACTTA
1 GTATCGATA-CTTTTTGCGTGCAAATTGTTTAAGATGCATACTGGAATAAAAGTATCGATACTTA
*
1071691 TATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTCAACCGGTAGATTTTTACCGTTT
65 TATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTCAACCGATAGATTTTTACCGTTT
* * * *
1071756 TCATTGTAAATTTACCTATTTCTTTAAAGAAATAGGTTTTCAAAATTACAAGTATTTATATTTGT
130 TCATTGTAAATTTACCTATTACTTTAAAGAAATAGG-TTTCGAAATTACAAGTATTGATACTTGT
1071821 TTATATGT
194 TTATATGT
* ** * * *
1071829 GTATCGATACTTTTTGCATGCAAATTGTTTAAGATTTATAATGGACTAAAAGTATCGATACATAT
1 GTATCGATACTTTTTGCGTGCAAATTGTTTAAGATGCATACTGGAATAAAAGTATCGATACTTAT
* * * * *
1071894 ATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTCAACGGGTATATTTTTTCCATTTT
66 ATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTCAACCGATAGATTTTTACCGTTTT
* *
1071959 CATTGTAAATTTACCTATTACTTTAAA-ATAAAAGGTTTCGAAATT-CTAAGTATCGATACTT-T
131 CATTGTAAATTTACCTATTACTTTAAAGA-AATAGGTTTCGAAATTAC-AAGTATTGATACTTGT
*
1072021 TTATATAT
194 TTATATGT
* * *
1072029 GTATCGCTACTTTTTTGTGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTA
1 GTATCGATAC-TTTTTGCGTGCAAATTGTTTAAGATGCATACTGGAATAAAAGTATCGATACTTA
* * * * * *
1072094 AATAATACGTATAGATACTTTATGTTTACGCCCATTATCATTGAACCGATAAATTTTTACCGTTT
65 TATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTCAACCGATAGATTTTTACCGTTT
* * * * * *
1072159 CCATTATATATTTACCTATTACTGTAAAGTAAT-GTGTTTCGAAATTACAAGTATCGATACTT-T
130 TCATTGTAAATTTACCTATTACTTTAAAGAAATAG-GTTTCGAAATTACAAGTATTGATACTTGT
* *
1072222 ATATATGA
194 TTATATGT
1072230 GTAT
1 GTAT
1072234 AAATAACCCT
Statistics
Matches: 528, Mismatches: 70, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
200 28 0.05
201 321 0.61
202 162 0.31
203 17 0.03
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.42
Consensus pattern (201 bp):
GTATCGATACTTTTTGCGTGCAAATTGTTTAAGATGCATACTGGAATAAAAGTATCGATACTTAT
ATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTCAACCGATAGATTTTTACCGTTTT
CATTGTAAATTTACCTATTACTTTAAAGAAATAGGTTTCGAAATTACAAGTATTGATACTTGTTT
ATATGT
Found at i:1072178 original size:403 final size:402
Alignment explanation
Indices: 1071426--1072212 Score: 1110
Period size: 403 Copynumber: 2.0 Consensus size: 402
1071416 GAAATTATAA
* * ** * * *
1071426 GTATTGATACTTTTTGCGTGCAAATTGTTTGTGATGCATATTAGAATACAAGTATCGATACTTAT
1 GTATCGATACTTTTTGCATGCAAATTGTTTAAGATGCATAATAGAATAAAAGTATCGATACATAT
* *
1071491 ATAATAAGTATCAATACTTGATGTTTATGCCTATTATCATTAAACCGATAGATTTTTACCGTTTA
66 ATAATAAGTATCAATACTTGATGTTTACGCCTATTATCATTAAACCGATAGATTTTTACCATTTA
* * *
1071556 TATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATTGATACTTGTTA
131 TATTGTAAATTTACCTATTACTTTAAAATAAAAGGTTTCGAAATTATAAGTATCGATACTTGTTA
* * **
1071621 TATGTGTATCGATATTTTTTTACGTGCAAATTGTTTAAGATGCATACTGTTATAAAAGTATCGAT
196 TATATGTATCGATACTTTTTTACGTGCAAATTGTTTAAGATGCATACTGGAATAAAAGTATCGAT
* * * * *
1071686 ACTTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTCAACCGGTAGATTTTTAC
261 ACTTAAATAATAAGTATAGATACTTTATGTTTACGCCCATTATCATTCAACCGATAAATTTTTAC
* * * *
1071751 CGTTTTCATTGTAAATTTACCTATTTCTTTAAAGAAATAG-GTTTTCAAAATTACAAGTATTTAT
326 CGTTTCCATTATAAATTTACCTATTACTGTAAAGAAAT-GTG-TTTCAAAATTACAAGTATTTAT
1071815 ATTTGTTTATATGT
389 ATTTGTTTATATGT
** * *
1071829 GTATCGATACTTTTTGCATGCAAATTGTTTAAGATTTATAATGGACTAAAAGTATCGATACATAT
1 GTATCGATACTTTTTGCATGCAAATTGTTTAAGATGCATAATAGAATAAAAGTATCGATACATAT
* * * * * * *
1071894 ATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTCAACGGGTATATTTTTTCCATTT-
66 ATAATAAGTATCAATACTTGATGTTTACGCCTATTATCATTAAACCGATAGATTTTTACCATTTA
* *
1071958 TCATTGTAAATTTACCTATTACTTTAAAATAAAAGGTTTCGAAATTCTAAGTATCGATACTTTTT
131 T-ATTGTAAATTTACCTATTACTTTAAAATAAAAGGTTTCGAAATTATAAGTATCGATACTTGTT
* ** *
1072023 ATATATGTATCGCTACTTTTTTGTGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGA
195 ATATATGTATCGATACTTTTTTACGTGCAAATTGTTTAAGATGCATACTGGAATAAAAGTATCGA
* *
1072088 TACTTAAATAATACGTATAGATACTTTATGTTTACGCCCATTATCATTGAACCGATAAATTTTTA
260 TACTTAAATAATAAGTATAGATACTTTATGTTTACGCCCATTATCATTCAACCGATAAATTTTTA
* * *
1072153 CCGTTTCCATTATATATTTACCTATTACTGTAAAGTAATGTGTTTCGAAATTACAAGTAT
325 CCGTTTCCATTATAAATTTACCTATTACTGTAAAGAAATGTGTTTCAAAATTACAAGTAT
1072213 CGATACTTTA
Statistics
Matches: 335, Mismatches: 47, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
402 19 0.06
403 316 0.94
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.42
Consensus pattern (402 bp):
GTATCGATACTTTTTGCATGCAAATTGTTTAAGATGCATAATAGAATAAAAGTATCGATACATAT
ATAATAAGTATCAATACTTGATGTTTACGCCTATTATCATTAAACCGATAGATTTTTACCATTTA
TATTGTAAATTTACCTATTACTTTAAAATAAAAGGTTTCGAAATTATAAGTATCGATACTTGTTA
TATATGTATCGATACTTTTTTACGTGCAAATTGTTTAAGATGCATACTGGAATAAAAGTATCGAT
ACTTAAATAATAAGTATAGATACTTTATGTTTACGCCCATTATCATTCAACCGATAAATTTTTAC
CGTTTCCATTATAAATTTACCTATTACTGTAAAGAAATGTGTTTCAAAATTACAAGTATTTATAT
TTGTTTATATGT
Found at i:1073080 original size:43 final size:43
Alignment explanation
Indices: 1073032--1073121 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
1073022 AACCTTTTAA
* **
1073032 AATTTAATGACCAAAATAGAAGAGAGAAAATAGTTGAGTGATG
1 AATTTAATGACCAAAATAGAAAAGAGAAAATAACTGAGTGATG
*
1073075 AATTTAGTGACCAAAATAGAAAAGAGAAAATAACTGAGTGATG
1 AATTTAATGACCAAAATAGAAAAGAGAAAATAACTGAGTGATG
1073118 AATT
1 AATT
1073122 GTATAATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.23
Consensus pattern (43 bp):
AATTTAATGACCAAAATAGAAAAGAGAAAATAACTGAGTGATG
Found at i:1073391 original size:2 final size:2
Alignment explanation
Indices: 1073384--1073414 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1073374 AAATAAATAA
1073384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1073415 AAAGTTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1073517 original size:2 final size:2
Alignment explanation
Indices: 1073510--1073541 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1073500 AATGAACTTT
1073510 TA TA TA TA 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
1073542 AAAGTTCATT
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):
TA
Found at i:1077978 original size:29 final size:29
Alignment explanation
Indices: 1077936--1077993 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1077926 TTATAACAAC
*
1077936 ATTTTAATTGAGTGACT-TATTTATAATTT
1 ATTTTAACTGAGTGA-TATATTTATAATTT
1077965 ATTTTAACTGAGTGATATATTTATAATTT
1 ATTTTAACTGAGTGATATATTTATAATTT
1077994 TTAGAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.53
Consensus pattern (29 bp):
ATTTTAACTGAGTGATATATTTATAATTT
Found at i:1081430 original size:21 final size:20
Alignment explanation
Indices: 1081406--1081453 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1081396 ACATAAACTT
*
1081406 TTTAGTGATATATCACTTCAA
1 TTTAGTGATATATCA-TACAA
**
1081427 TTTAAAAGATATATCATACAA
1 TTT-AGTGATATATCATACAA
1081448 TTTAGT
1 TTTAGT
1081454 AATGTTTTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
20 1 0.05
21 10 0.48
22 10 0.48
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (20 bp):
TTTAGTGATATATCATACAA
Found at i:1081636 original size:121 final size:121
Alignment explanation
Indices: 1081377--1081823 Score: 492
Period size: 121 Copynumber: 3.7 Consensus size: 121
1081367 ATCGTTGAAT
* *
1081377 GACCATTTAATGCACAATTACATAAACTTTTTAGTGATATATCACTTCAATTTAAAAGATATATC
1 GACCATTTAATGCACAATGACATAAACTTTTCAGTGATATATCACTTCAATTT-AAAGATATATC
* * * * * * * *
1081442 ATACAATTTAGTAATGTTTTTGACCAATTATTTAATG-AAAACGTATTTGTTCTT-AGA
65 ATACAATTGAATGATGTTTGTGACCTATTTTTTAATGAAAAACGTCTTT-TT-TTCAAA
* **
1081499 GACCATTTAATGCACAATAACATAAA-TTTTCCAGTGATATATCACTTCAATTTAGTGATATATC
1 GACCATTTAATGCACAATGACATAAACTTTT-CAGTGATATATCACTTCAATTTAAAGATATATC
* *
1081563 ATACCATTGAATGATGTTTGTGACCTATTTTTTAATGAAAAACATCTTTTTTTCAAA
65 ATACAATTGAATGATGTTTGTGACCTATTTTTTAATGAAAAACGTCTTTTTTTCAAA
* * * *
1081620 GACCATTTAATGCACAATGGCATAAACTTTTCAGTGATAAATCACTTCAATTCAATGATATATCA
1 GACCATTTAATGCACAATGACATAAACTTTTCAGTGATATATCACTTCAATTTAAAGATATATCA
* * * * * * *
1081685 TACCATTGAATGAT-ATTGTTGA-CTAATGTTTTAATGAAAAATGTCATTTTCTCATA
66 TACAATTGAATGATGTTTG-TGACCT-ATTTTTTAATGAAAAACGTCTTTTTTTCAAA
* * * * *
1081741 GACCATTTAATACAGAATGACAAAAACTTTTCAGTGCT-TAATCACTTGAATTTAAAGATATATC
1 GACCATTTAATGCACAATGACATAAACTTTTCAGTGATAT-ATCACTTCAATTTAAAGATATATC
* *
1081805 AGACAAATGAATGATGTTT
65 ATACAATTGAATGATGTTT
1081824 TAACCATATT
Statistics
Matches: 278, Mismatches: 39, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
120 7 0.03
121 210 0.76
122 61 0.22
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (121 bp):
GACCATTTAATGCACAATGACATAAACTTTTCAGTGATATATCACTTCAATTTAAAGATATATCA
TACAATTGAATGATGTTTGTGACCTATTTTTTAATGAAAAACGTCTTTTTTTCAAA
Found at i:1081803 original size:242 final size:243
Alignment explanation
Indices: 1081377--1081823 Score: 564
Period size: 242 Copynumber: 1.8 Consensus size: 243
1081367 ATCGTTGAAT
* * *
1081377 GACCATTTAATGCACAATTACATAAACTTTTTAGTGATATATCACTTCAATTTAAAAGATATATC
1 GACCATTTAATGCACAATGACATAAACTTTTCAGTGATAAATCACTTCAATTTAAAAGATATATC
* * * * *
1081442 ATACAATTTAGTAATGTTTTTGACCAATTATTTAATGAAAACGTATTTGTTCTTAGAGACCATTT
66 ATACAATTGAATAATATTGTTGACCAATTATTTAATGAAAACGTATTTGTTCTCAGAGACCATTT
* * ** * * *
1081507 AATGCACAATAACATAAATTTTCCAGTGATATATCACTTCAATTTAGTGATATATCATACCATTG
131 AATACACAATAACAAAAATTTTCCAGTGATATATCACTTCAATTTAAAGATATATCAGACAAATG
1081572 AATGATGTTTGTGACCTATTTTTTAATGAAAAACATCTTTTTTTCAAA
196 AATGATGTTTGTGACCTATTTTTTAATGAAAAACATCTTTTTTTCAAA
* * *
1081620 GACCATTTAATGCACAATGGCATAAACTTTTCAGTGATAAATCACTTCAA-TTCAATGATATATC
1 GACCATTTAATGCACAATGACATAAACTTTTCAGTGATAAATCACTTCAATTTAAAAGATATATC
* * * * *
1081684 ATACCATTGAATGATATTGTTGACTAATGT-TTTAATGAAAAATGTCA-TT-TTCTCATAGACCA
66 ATACAATTGAATAATATTGTTGACCAAT-TATTTAATG-AAAACGT-ATTTGTTCTCAGAGACCA
* * * *
1081746 TTTAATACAGAATGACAAAAACTTTT-CAGTGCT-TAATCACTTGAATTTAAAGATATATCAGAC
128 TTTAATACACAATAACAAAAA-TTTTCCAGTGATAT-ATCACTTCAATTTAAAGATATATCAGAC
1081809 AAATGAATGATGTTT
191 AAATGAATGATGTTT
1081824 TAACCATATT
Statistics
Matches: 172, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
241 1 0.01
242 111 0.65
243 59 0.34
244 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (243 bp):
GACCATTTAATGCACAATGACATAAACTTTTCAGTGATAAATCACTTCAATTTAAAAGATATATC
ATACAATTGAATAATATTGTTGACCAATTATTTAATGAAAACGTATTTGTTCTCAGAGACCATTT
AATACACAATAACAAAAATTTTCCAGTGATATATCACTTCAATTTAAAGATATATCAGACAAATG
AATGATGTTTGTGACCTATTTTTTAATGAAAAACATCTTTTTTTCAAA
Found at i:1082459 original size:26 final size:26
Alignment explanation
Indices: 1082430--1082492 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
1082420 GCTTCTATTG
* *
1082430 TAATGTAATGTACGAGCTAGTGTTTC
1 TAATGTAATGTAAGAGCTAATGTTTC
* **
1082456 TAATGTAATGCAAGATTTAATGTTTC
1 TAATGTAATGTAAGAGCTAATGTTTC
*
1082482 TAATATAATGT
1 TAATGTAATGT
1082493 TTGTATTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.41
Consensus pattern (26 bp):
TAATGTAATGTAAGAGCTAATGTTTC
Found at i:1094420 original size:31 final size:33
Alignment explanation
Indices: 1094375--1094471 Score: 108
Period size: 33 Copynumber: 3.0 Consensus size: 33
1094365 CAAAGATGAA
* * **
1094375 AATAAGTTGGCCACCTACCAA-A-GTTTTTTCC
1 AATAAGTTGACCACCAACCAAGATGAATTTTCC
* *
1094406 AATAAATTGTCCACCAACCAAGATGAATTTTCC
1 AATAAGTTGACCACCAACCAAGATGAATTTTCC
*
1094439 AATAAGTTGACCACCAACCAAGATAAAATTTTC
1 AATAAGTTGACCACCAACCAAGAT-GAATTTTC
1094472 AACTTGTCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 18 0.33
32 1 0.02
33 29 0.53
34 7 0.13
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (33 bp):
AATAAGTTGACCACCAACCAAGATGAATTTTCC
Found at i:1094442 original size:33 final size:34
Alignment explanation
Indices: 1094400--1094471 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
1094390 TACCAAAGTT
* *
1094400 TTTTCCAATAAATTGTCCACCAACCAAGAT-GAA
1 TTTTCCAATAAATTGACCACCAACCAAGATAAAA
*
1094433 TTTTCCAATAAGTTGACCACCAACCAAGATAAAA
1 TTTTCCAATAAATTGACCACCAACCAAGATAAAA
1094467 TTTTC
1 TTTTC
1094472 AACTTGTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 28 0.80
34 7 0.20
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (34 bp):
TTTTCCAATAAATTGACCACCAACCAAGATAAAA
Found at i:1099893 original size:36 final size:34
Alignment explanation
Indices: 1099848--1100142 Score: 175
Period size: 36 Copynumber: 8.6 Consensus size: 34
1099838 TTTAAAAAAG
* *
1099848 AAAACATTTTGAAAATATGGGTAATATATAGTTTTT
1 AAAACATTTTGAAAATAT--ATAACATATAGTTTTT
* *
1099884 TAAATATTTTTGAAAACTATATAACATATAGTTTTT
1 AAAACA-TTTTGAAAA-TATATAACATATAGTTTTT
1099920 AAAACATTTTAGAAAATATAT-A-A-ATAG-TTTT
1 AAAACATTTT-GAAAATATATAACATATAGTTTTT
* * *
1099951 AAAATCATTTTAAAAACTTATATAATATATAGTTTTA
1 AAAA-CATTTTGAAAA--TATATAACATATAGTTTTT
* *
1099988 AAAACATTTTTGAATAAATTATATAATATATAGTTTTA
1 AAAACA-TTTTG-A-AAA-TATATAACATATAGTTTTT
* * * *
1100026 AAAACGTTTTTTAAAA-A-ACTTATATAATA-TTTTT
1 AAAAC-ATTTTGAAAATATA-TAACAT-ATAGTTTTT
*
1100060 AAAACATTTTGAAAACTATAT-A-ATATAGTTTTG
1 AAAACATTTTGAAAA-TATATAACATATAGTTTTT
** * **
1100093 AAAAC-TTTT-TTAA-ATATAATATATAGTTTAA
1 AAAACATTTTGAAAATATATAACATATAGTTTTT
*
1100124 AAAATATTTTG-AAATATAT
1 AAAACATTTTGAAAATATAT
1100143 GTATTATATA
Statistics
Matches: 212, Mismatches: 22, Indels: 53
0.74 0.08 0.18
Matches are distributed among these distances:
29 4 0.02
30 1 0.00
31 27 0.13
32 23 0.11
33 30 0.14
34 18 0.08
35 15 0.07
36 37 0.17
37 21 0.10
38 33 0.16
39 3 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (34 bp):
AAAACATTTTGAAAATATATAACATATAGTTTTT
Found at i:1100139 original size:31 final size:34
Alignment explanation
Indices: 1099885--1100142 Score: 118
Period size: 38 Copynumber: 7.5 Consensus size: 34
1099875 ATAGTTTTTT
1099885 AAATATTTTTGAAA-ACTATATAACATATAGTTTTTAAA
1 AAATA-TTTTGAAATA-TATAT-A-ATATAG-TTTTAAA
* *
1099923 ACAT-TTTAGAAA-ATATATAA-ATAGTTTT--A
1 AAATATTTTGAAATATATATAATATAGTTTTAAA
*
1099952 AAATCATTTT-AAAAACTTATATAATATATAGTTTTAAA
1 AAAT-ATTTTGAAATA--TATAT-A-ATATAGTTTTAAA
*
1099990 AACAT-TTTTGAATAAATTATATAATATATAGTTTTAAA
1 AA-ATATTTTGAA-ATA-TATAT-A-ATATAGTTTTAAA
* * * *
1100028 AACGTTTTTTAAAAAACTTATATAATAT--TTTT--A
1 AA-ATATTTTGAAATA--TATATAATATAGTTTTAAA
* *
1100061 AAACATTTTGAAA-ACTATATAATATAGTTTTGAA
1 AAATATTTTGAAATA-TATATAATATAGTTTTAAA
* *
1100095 AACT-TTTTTAAATATA-AT-ATATAG-TTTAAA
1 AAATATTTTGAAATATATATAATATAGTTTTAAA
1100125 AAATATTTTGAAATATAT
1 AAATATTTTGAAATATAT
1100143 GTATTATATA
Statistics
Matches: 181, Mismatches: 17, Indels: 50
0.73 0.07 0.20
Matches are distributed among these distances:
29 4 0.02
30 21 0.12
31 26 0.14
32 17 0.09
33 18 0.10
34 6 0.03
35 10 0.06
36 16 0.09
37 8 0.04
38 38 0.21
39 17 0.09
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (34 bp):
AAATATTTTGAAATATATATAATATAGTTTTAAA
Found at i:1100199 original size:14 final size:15
Alignment explanation
Indices: 1100174--1100202 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1100164 ATCAGTATTA
1100174 TTATTATTTTCTTTT
1 TTATTATTTTCTTTT
1100189 TTATT-TTTTCTTTT
1 TTATTATTTTCTTTT
1100203 ATGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (15 bp):
TTATTATTTTCTTTT
Found at i:1104779 original size:32 final size:31
Alignment explanation
Indices: 1104743--1104811 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1104733 TTAGACTCTT
1104743 AAAATTAAAAAAAAAAATTAATTCGGTCTCCC
1 AAAATT-AAAAAAAAAATTAATTCGGTCTCCC
***
1104775 AAAATTTTTAAAAAAATTAATTCGGTCTCCC
1 AAAATTAAAAAAAAAATTAATTCGGTCTCCC
1104806 AAAATT
1 AAAATT
1104812 TTTAAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 28 0.82
32 6 0.18
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30
Consensus pattern (31 bp):
AAAATTAAAAAAAAAATTAATTCGGTCTCCC
Found at i:1104791 original size:31 final size:31
Alignment explanation
Indices: 1104753--1104819 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
1104743 AAAATTAAAA
1104753 AAAAAAATTAATTCGGTCTCCCAAAATTTTT
1 AAAAAAATTAATTCGGTCTCCCAAAATTTTT
1104784 AAAAAAATTAATTCGGTCTCCCAAAATTTTT
1 AAAAAAATTAATTCGGTCTCCCAAAATTTTT
1104815 AAAAA
1 AAAAA
1104820 TTTAGATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (31 bp):
AAAAAAATTAATTCGGTCTCCCAAAATTTTT
Found at i:1106369 original size:34 final size:30
Alignment explanation
Indices: 1106326--1106400 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 30
1106316 GGTTTTTCGA
*
1106326 AAAATGAATTACTGGCTGGAATTTGAATTACTGT
1 AAAATGAATTAC---CTGGAATTTGAATT-CTGG
1106360 AAAATGAATTA-CTGGAATTTGAATTCTGG
1 AAAATGAATTACCTGGAATTTGAATTCTGG
1106389 AAAATGAATTAC
1 AAAATGAATTAC
1106401 ATTTCTGGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 14 0.36
30 14 0.36
34 11 0.28
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (30 bp):
AAAATGAATTACCTGGAATTTGAATTCTGG
Found at i:1106377 original size:30 final size:29
Alignment explanation
Indices: 1106341--1106400 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
1106331 GAATTACTGG
*
1106341 CTGGAATTTGAATTACTGTAAAATGAATTA
1 CTGGAATTTGAATT-CTGGAAAATGAATTA
1106371 CTGGAATTTGAATTCTGGAAAATGAATTA
1 CTGGAATTTGAATTCTGGAAAATGAATTA
1106400 C
1 C
1106401 ATTTCTGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (29 bp):
CTGGAATTTGAATTCTGGAAAATGAATTA
Found at i:1106396 original size:14 final size:15
Alignment explanation
Indices: 1106349--1106400 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
1106339 GGCTGGAATT
*
1106349 TGAATTACTGTAAAA
1 TGAATTACTGGAAAA
**
1106364 TGAATTACTGGAATT
1 TGAATTACTGGAAAA
1106379 TGAATT-CTGGAAAA
1 TGAATTACTGGAAAA
1106393 TGAATTAC
1 TGAATTAC
1106401 ATTTCTGGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAAAA
Found at i:1106783 original size:23 final size:23
Alignment explanation
Indices: 1106734--1106796 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1106724 GTGTTATATT
* **
1106734 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
1106757 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
1106780 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
1106797 AAATATATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:1106818 original size:19 final size:20
Alignment explanation
Indices: 1106772--1106882 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 20
1106762 TTAAATATCT
1106772 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
1106791 ATATATAAATATATTA-TTCA
1 TTAT-TAAATATATTATTTAA
* **
1106811 TTATTAAATATATAATTTTT
1 TTATTAAATATATTATTTAA
*
1106831 TTATT--ATATATTATTAAA
1 TTATTAAATATATTATTTAA
* * *
1106849 ATA-AAAATATAATATCTTATA
1 TTATTAAATATATTAT-TTA-A
1106870 TTATTATAATATA
1 TTATTA-AATATA
1106883 ATTGATTATT
Statistics
Matches: 67, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
18 11 0.16
19 21 0.31
20 19 0.28
21 9 0.13
22 1 0.01
23 6 0.09
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:1106834 original size:27 final size:26
Alignment explanation
Indices: 1106781--1106843 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
1106771 TTTATTAAAA
1106781 TATTATTTAAATATATAAATATATTAT
1 TATTA-TTAAATATATAAATATATTAT
* * *
1106808 TCATTATTAAATATATAATTTTTTTAT
1 T-ATTATTAAATATATAAATATATTAT
1106835 TATATATTA
1 TAT-TATTA
1106844 TTAAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 2 0.06
27 25 0.81
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTATTAAATATATAAATATATTAT
Found at i:1106909 original size:17 final size:17
Alignment explanation
Indices: 1106865--1106922 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
1106855 ATATAATATC
1106865 TTATATTATTATAATATAA
1 TTATATTATTATAA-AT-A
1106884 TTGATTATT-TTATATAATA
1 TT-A-TATTATTATA-AATA
1106903 TTATATTATTATAAATA
1 TTATATTATTATAAATA
1106920 TTA
1 TTA
1106923 ATAAATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 11 0.31
18 6 0.17
19 5 0.14
20 8 0.23
21 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTATATTATTATAAATA
Found at i:1107223 original size:41 final size:42
Alignment explanation
Indices: 1107106--1107211 Score: 178
Period size: 42 Copynumber: 2.5 Consensus size: 42
1107096 ATTACGTTCA
* *
1107106 GGAAAACCAATTACGTGAAACAAATACTGGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAACAAACACTGGAAAACATTTTCC
*
1107148 GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAACAAACACTGGAAAACATTTTCC
1107190 -GAAAACGAATTACGTGAAACAA
1 GGAAAACGAATTACGTGAAACAA
1107212 CACATTTAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
41 22 0.36
42 39 0.64
ACGTcount: A:0.47, C:0.18, G:0.17, T:0.18
Consensus pattern (42 bp):
GGAAAACGAATTACGTGAAACAAACACTGGAAAACATTTTCC
Found at i:1107299 original size:21 final size:22
Alignment explanation
Indices: 1107262--1107310 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1107252 ATTAATTTTT
1107262 AAATTTCAAAATGTTTTAATTA-
1 AAATTTCAAAATGTTTTAA-TAC
*
1107284 AAATTTTAAAAT-TTTTAATAC
1 AAATTTCAAAATGTTTTAATAC
1107305 AAATTT
1 AAATTT
1107311 AGTTATGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 12 0.48
22 11 0.44
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATTTCAAAATGTTTTAATAC
Found at i:1108760 original size:19 final size:19
Alignment explanation
Indices: 1108736--1108787 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1108726 AAAACTCTGA
1108736 GTGCATCGATGCATAGTAT
1 GTGCATCGATGCATAGTAT
1108755 GTGCATCGATGCATAGTAT
1 GTGCATCGATGCATAGTAT
1108774 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1108788 GAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATAGTAT
Found at i:1110277 original size:13 final size:15
Alignment explanation
Indices: 1110259--1110290 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1110249 ATATTTGACT
1110259 ATGGGATAT-TTT-A
1 ATGGGATATATTTCA
1110272 ATGGGATATATTTCA
1 ATGGGATATATTTCA
1110287 ATGG
1 ATGG
1110291 AAATTGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.31, C:0.03, G:0.25, T:0.41
Consensus pattern (15 bp):
ATGGGATATATTTCA
Found at i:1110356 original size:12 final size:12
Alignment explanation
Indices: 1110339--1110364 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1110329 GAATTTCTCA
1110339 TAAATTCAATTT
1 TAAATTCAATTT
1110351 TAAATTCAATTT
1 TAAATTCAATTT
1110363 TA
1 TA
1110365 TTAGAAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATTCAATTT
Found at i:1113549 original size:23 final size:23
Alignment explanation
Indices: 1113526--1113573 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
1113516 ACGATTAAGA
*
1113526 AAATGTTTTAAAACT-GATAAAG
1 AAATGTTTTAAAAATGGATAAAG
1113548 AAATGTTTTAAAAATGGATAAA-
1 AAATGTTTTAAAAATGGATAAAG
1113570 AAAT
1 AAAT
1113574 TTTAAGCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (23 bp):
AAATGTTTTAAAAATGGATAAAG
Found at i:1114775 original size:12 final size:11
Alignment explanation
Indices: 1114753--1114787 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1114743 TTCTCTACTT
1114753 TACATTACATA
1 TACATTACATA
1114764 TACATATACATA
1 TACAT-TACATA
*
1114776 TACATTATATA
1 TACATTACATA
1114787 T
1 T
1114788 GTCTGTGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (11 bp):
TACATTACATA
Found at i:1117869 original size:6 final size:6
Alignment explanation
Indices: 1117818--1117860 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
1117808 CCGCTCTCAC
* *
1117818 CTTCAT CTTC-G CTATCAT CTCCAT CTTCAT CTTCAT CTTCAT C
1 CTTCAT CTTCAT CT-TCAT CTTCAT CTTCAT CTTCAT CTTCAT C
1117861 ATCTTCATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 2 0.06
6 27 0.87
7 2 0.06
ACGTcount: A:0.16, C:0.37, G:0.02, T:0.44
Consensus pattern (6 bp):
CTTCAT
Found at i:1118859 original size:71 final size:70
Alignment explanation
Indices: 1118771--1119003 Score: 242
Period size: 71 Copynumber: 3.3 Consensus size: 70
1118761 AAAAAACAAA
* * *
1118771 TTTCATCTCACTTGAGACAATCTCTTTGAAACAAAAATTACATTTCACTTGAGATATTTTCCCTT
1 TTTCATCTCACTCGAGACAAT-TCTTTGAAACAAAAATTTCATCTCACTTGAGATATTTTCCCTT
*
1118836 TAAAAT
65 GAAAAT
* * * *
1118842 TTTCGTCTCACTCGAGACAGTTTTTCTCGAAAC-AAAATTTCATCTCACTTGAGTTATTTTCCCT
1 TTTCATCTCACTCGAGACAATTCTT-T-GAAACAAAAATTTCATCTCACTTGAGATATTTTCCCT
*
1118906 TGAAAAG
64 TGAAAAT
* * *
1118913 TTTCATCTTACTTGAGA-AATGTTCTCTT-AAA-AGAAAATTTCATCTCGCTTGAGATATTTTCC
1 TTTCATCTCACTCGAGACAA--TTCT-TTGAAACA-AAAATTTCATCTCACTTGAGATATTTTCC
1118975 C-TGAAAATT
62 CTTGAAAA-T
1118984 TTTCATCTCACTTCGAGACA
1 TTTCATCTCAC-TCGAGACA
1119004 GTATCTCTCG
Statistics
Matches: 133, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
70 13 0.10
71 104 0.78
72 14 0.11
73 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (70 bp):
TTTCATCTCACTCGAGACAATTCTTTGAAACAAAAATTTCATCTCACTTGAGATATTTTCCCTTG
AAAAT
Found at i:1118919 original size:34 final size:34
Alignment explanation
Indices: 1118815--1119001 Score: 128
Period size: 34 Copynumber: 5.3 Consensus size: 34
1118805 AAATTACATT
* * *
1118815 TCACTTGAGATATTTTCCCTTTAAAATTTTCGTC
1 TCACTTGAGATATTTTCCCTTGAAAAGTTTCATC
* * * * *
1118849 TCACTCGAGACAGTTTT-TCTCGAAACAAAATTTCATC
1 TCACTTGAGATA-TTTTCCCTTG--A-AAAGTTTCATC
*
1118886 TCACTTGAGTTATTTTCCCTTGAAAAGTTTCATC
1 TCACTTGAGATATTTTCCCTTGAAAAGTTTCATC
* * * *
1118920 TTACTTGAGAAATGTTCTCTT-AAAAGAAAATTTCATC
1 TCACTTGAGATATTTTCCCTTGAAAAG----TTTCATC
* *
1118957 TCGCTTGAGATATTTTCCC-TGAAAATTTTTCATC
1 TCACTTGAGATATTTTCCCTTGAAAA-GTTTCATC
1118991 TCACTTCGAGA
1 TCACTT-GAGA
1119002 CAGTATCTCT
Statistics
Matches: 116, Mismatches: 25, Indels: 23
0.71 0.15 0.14
Matches are distributed among these distances:
33 5 0.04
34 50 0.43
35 9 0.08
36 6 0.05
37 46 0.40
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.40
Consensus pattern (34 bp):
TCACTTGAGATATTTTCCCTTGAAAAGTTTCATC
Found at i:1118968 original size:142 final size:143
Alignment explanation
Indices: 1118771--1119036 Score: 353
Period size: 142 Copynumber: 1.9 Consensus size: 143
1118761 AAAAAACAAA
*
1118771 TTTCATCTCACTTGAGACAATCTCTTTGAAACAAAAATTACATTTCACTTGAGATATTTTCCCTT
1 TTTCATCTCACTTGAGACAATCTCTTTGAAACAAAAATTACATCTCACTTGAGATATTTTCCC-T
* * * * * *
1118836 TAAAA-TTTTCGTCTCAC-TCGAGACAGTTTTTCTCGAAACAAAATTTCATCTCACTTGAGTTAT
65 GAAAATTTTTCATCTCACTTCGAGACAGTATCTCTCGAAACAAAACTGCATCTCACTTGAGTTAT
1118899 TTTCCCTTGAAAAG
130 TTTCCCTTGAAAAG
* * * *
1118913 TTTCATCTTACTTGAGA-AATGTTCTCTT-AAA-AGAAAATTTCATCTCGCTTGAGATATTTTCC
1 TTTCATCTCACTTGAGACAAT-CTCT-TTGAAACA-AAAATTACATCTCACTTGAGATATTTTCC
*
1118975 CTGAAAATTTTTCATCTCACTTCGAGACAGTATCTCTCGAAATAAAACTGCATCTCACTTGA
63 CTGAAAATTTTTCATCTCACTTCGAGACAGTATCTCTCGAAACAAAACTGCATCTCACTTGA
1119037 TTTTATCTTG
Statistics
Matches: 107, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
141 9 0.08
142 60 0.56
143 38 0.36
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (143 bp):
TTTCATCTCACTTGAGACAATCTCTTTGAAACAAAAATTACATCTCACTTGAGATATTTTCCCTG
AAAATTTTTCATCTCACTTCGAGACAGTATCTCTCGAAACAAAACTGCATCTCACTTGAGTTATT
TTCCCTTGAAAAG
Found at i:1120277 original size:28 final size:28
Alignment explanation
Indices: 1120237--1120299 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
1120227 CTTTTCTTAC
1120237 TGCTTGTAGATCAACATATGTAGTTTGA
1 TGCTTGTAGATCAACATATGTAGTTTGA
1120265 TGCTTGTAGATCAACATATGTAGTTTGA
1 TGCTTGTAGATCAACATATGTAGTTTGA
1120293 TGCTTGT
1 TGCTTGT
1120300 GTGAGTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.41
Consensus pattern (28 bp):
TGCTTGTAGATCAACATATGTAGTTTGA
Found at i:1122278 original size:2 final size:2
Alignment explanation
Indices: 1122211--1122260 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
1122201 GATTTAAAAA
* *
1122211 AT AT AT -T AT AT AT -T AT AT AT AT -T TT TT GAT 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
1122251 AT AT AT AT AT
1 AT AT AT AT AT
1122261 GCATTTTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
1 3 0.07
2 39 0.91
3 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:1122289 original size:16 final size:17
Alignment explanation
Indices: 1122264--1122333 Score: 54
Period size: 17 Copynumber: 4.0 Consensus size: 17
1122254 TATATATGCA
1122264 TTTTGAAA-ATATATAAT
1 TTTTGAAATATATAT-AT
*
1122281 TTTTGAAATGTATTATAT
1 TTTTGAAATATA-TATAT
* **
1122299 TTTGGAGAATATATAGCT
1 TTTTGA-AATATATATAT
1122317 TTTT-AATATATATATAT
1 TTTTGAA-ATATATATAT
1122334 ATATATATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
16 1 0.02
17 17 0.41
18 15 0.37
19 8 0.20
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (17 bp):
TTTTGAAATATATATAT
Found at i:1122301 original size:17 final size:18
Alignment explanation
Indices: 1122263--1122313 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
1122253 ATATATATGC
1122263 ATTTTGAAAATATATAAT
1 ATTTTGAAAATATATAAT
* *
1122281 -TTTTG-AAATGTATTAT
1 ATTTTGAAAATATATAAT
*
1122297 ATTTTGGAGAATATATA
1 ATTTT-GAAAATATATA
1122314 GCTTTTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
16 9 0.36
17 9 0.36
18 1 0.04
19 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (18 bp):
ATTTTGAAAATATATAAT
Found at i:1122327 original size:2 final size:2
Alignment explanation
Indices: 1122322--1122398 Score: 102
Period size: 2 Copynumber: 38.5 Consensus size: 2
1122312 TAGCTTTTTA
* *
1122322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T TT GAA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* *
1122364 AA AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1122399 AAATAAATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1122442 original size:13 final size:13
Alignment explanation
Indices: 1122426--1122451 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1122416 TAAATATATA
1122426 GTATGTATATTAT
1 GTATGTATATTAT
1122439 GTATGTATATTAT
1 GTATGTATATTAT
1122452 AATTATAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
GTATGTATATTAT
Found at i:1122479 original size:13 final size:12
Alignment explanation
Indices: 1122461--1122514 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
1122451 TAATTATAGG
*
1122461 TATATTATTATTT
1 TATATTAATA-TT
1122474 TATATTAATATT
1 TATATTAATATT
*
1122486 AATATTAATATT
1 TATATTAATATT
1122498 TATTATT-ATATT
1 TA-TATTAATATT
1122510 T-TATT
1 TATATT
1122515 TTTTTAGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.11
12 20 0.54
13 13 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATATTAATATT
Found at i:1122504 original size:25 final size:24
Alignment explanation
Indices: 1122462--1122509 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1122452 AATTATAGGT
*
1122462 ATATTATTATTTTATATTAATATTA
1 ATATTAATATTTTATATT-ATATTA
1122487 ATATTAATA-TTTATTATTATATT
1 ATATTAATATTTTA-TATTATATT
1122510 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATTAATATTTTATATTATATTA
Found at i:1126091 original size:30 final size:30
Alignment explanation
Indices: 1126057--1126114 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1126047 TTAAAGACTT
1126057 AATTTTTTCAATACTTATTATTAGGGTCCC
1 AATTTTTTCAATACTTATTATTAGGGTCCC
* *
1126087 AATTTTTTCAATATTTGTTATTAGGGTC
1 AATTTTTTCAATACTTATTATTAGGGTC
1126115 ATACTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (30 bp):
AATTTTTTCAATACTTATTATTAGGGTCCC
Found at i:1132239 original size:34 final size:34
Alignment explanation
Indices: 1132200--1132284 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
1132190 CGATTATATA
1132200 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
1132234 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
1132268 TATATATAAAATATTTT
1 TATATATATAATATTTT
1132285 CGGGTTCGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:1135187 original size:38 final size:36
Alignment explanation
Indices: 1135133--1135208 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 36
1135123 AATTTTTCAT
*
1135133 TATATTATTTTAATTATTATTATTATTAAATAA-AA
1 TATATTATTTTAATTATTATTATCATTAAATAATAA
1135168 TATATTATTATATATATTATTATTATCATTAAATAATAA
1 TATATTATT-T-TA-ATTATTATTATCATTAAATAATAA
1135207 TA
1 TA
1135209 ATAATAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
35 9 0.25
36 1 0.03
37 2 0.06
38 20 0.56
39 4 0.11
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (36 bp):
TATATTATTTTAATTATTATTATCATTAAATAATAA
Found at i:1136517 original size:12 final size:12
Alignment explanation
Indices: 1136487--1136530 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1136477 ATTACTTTTA
1136487 TATTTTAATTAT
1 TATTTTAATTAT
**
1136499 TGCTTTAATTAT
1 TATTTTAATTAT
1136511 TATTTT-ATTAT
1 TATTTTAATTAT
*
1136522 TATCTTAAT
1 TATTTTAAT
1136531 CATATATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:1138169 original size:35 final size:33
Alignment explanation
Indices: 1138103--1138204 Score: 116
Period size: 35 Copynumber: 3.0 Consensus size: 33
1138093 ATAAGAAGGC
*
1138103 CAAACCATTAACC-AAAAACAACCTGAAACATT
1 CAAACCATTGACCAAAAAACAACCTGAAACATT
*
1138135 CAAACCATTGACCAAAAATAGCAACCTGAGACATT
1 CAAACCATTGACCAAAAA-A-CAACCTGAAACATT
* * *
1138170 GAAACCATTGACCAAACACAATAACCTGAACCATT
1 CAAACCATTGACCAAA-A-AACAACCTGAAACATT
1138205 TCCCAAAGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
32 12 0.20
33 4 0.07
34 1 0.02
35 39 0.66
36 2 0.03
37 1 0.02
ACGTcount: A:0.48, C:0.27, G:0.08, T:0.17
Consensus pattern (33 bp):
CAAACCATTGACCAAAAAACAACCTGAAACATT
Found at i:1138574 original size:32 final size:32
Alignment explanation
Indices: 1138533--1138634 Score: 159
Period size: 32 Copynumber: 3.2 Consensus size: 32
1138523 AAACAATAAA
1138533 GGGCATCTTTGAAGATTCAACATCAAATATTG
1 GGGCATCTTTGAAGATTCAACATCAAATATTG
*
1138565 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTGAAGATTCAACATCAAATATTG
* * *
1138597 GGGCATCTTTGGAGATTCAATATCGAATATTG
1 GGGCATCTTTGAAGATTCAACATCAAATATTG
*
1138629 AGGCAT
1 GGGCAT
1138635 TCAATATCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (32 bp):
GGGCATCTTTGAAGATTCAACATCAAATATTG
Found at i:1138782 original size:33 final size:33
Alignment explanation
Indices: 1138742--1138864 Score: 165
Period size: 34 Copynumber: 3.7 Consensus size: 33
1138732 AAAAAATAAT
* *
1138742 TTTGTCTCACTTGAGATAATTTCTCAAAGCAAA
1 TTTGTCTCACTTGAGACAATTTCTCAAAACAAA
1138775 TTTGTCTCACTTGAGACAATTTCTCAAAACAAA
1 TTTGTCTCACTTGAGACAATTTCTCAAAACAAA
* **
1138808 TTCCGTCTTGCTTGAGACAATTTCTCAAAACAAA
1 TT-TGTCTCACTTGAGACAATTTCTCAAAACAAA
**
1138842 TTTCGTCTCGTTTGAGACAATTT
1 TTT-GTCTCACTTGAGACAATTT
1138865 TTCTCTGAGA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
33 33 0.41
34 47 0.59
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (33 bp):
TTTGTCTCACTTGAGACAATTTCTCAAAACAAA
Found at i:1139206 original size:40 final size:40
Alignment explanation
Indices: 1139162--1139281 Score: 119
Period size: 40 Copynumber: 3.1 Consensus size: 40
1139152 TCATTTCACT
1139162 ACATGTTGTTTTTCTTAAAACAACTTTCGTCTCGCTTGAG
1 ACATGTTGTTTTTCTTAAAACAACTTTCGTCTCGCTTGAG
* * * * *
1139202 ACATG-T-TTTAT-TAAAAACAAGACATTTCATTTCAC-T---
1 ACATGTTGTTTTTCTTAAAAC-A-AC-TTTCGTCTCGCTTGAG
1139238 ACATGTTGTTTTTCTTAAAACAACTTTCGTCTCGCTTGAG
1 ACATGTTGTTTTTCTTAAAACAACTTTCGTCTCGCTTGAG
1139278 ACAT
1 ACAT
1139282 TTTTTTACTC
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
36 13 0.22
37 10 0.17
38 10 0.17
39 10 0.17
40 17 0.28
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (40 bp):
ACATGTTGTTTTTCTTAAAACAACTTTCGTCTCGCTTGAG
Found at i:1139242 original size:36 final size:36
Alignment explanation
Indices: 1139130--1139244 Score: 101
Period size: 36 Copynumber: 3.1 Consensus size: 36
1139120 CTTGAGACAG
1139130 GTTTTATTAAAAACAAGACATTTCATTTCACTACAT
1 GTTTTATTAAAAACAAGACATTTCATTTCACTACAT
* * * * *
1139166 GTTGTTTTTCTTAAAAC-A-AC-TTTCGTCTCGCTTGAGACAT
1 G-T-TTTAT-TAAAAACAAGACATTTCATTTCAC-T---ACAT
1139206 GTTTTATTAAAAACAAGACATTTCATTTCACTACAT
1 GTTTTATTAAAAACAAGACATTTCATTTCACTACAT
1139242 GTT
1 GTT
1139245 GTTTTTCTTA
Statistics
Matches: 59, Mismatches: 10, Indels: 20
0.66 0.11 0.22
Matches are distributed among these distances:
36 16 0.27
37 10 0.17
38 10 0.17
39 10 0.17
40 13 0.22
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (36 bp):
GTTTTATTAAAAACAAGACATTTCATTTCACTACAT
Found at i:1139334 original size:77 final size:76
Alignment explanation
Indices: 1139045--1139404 Score: 399
Period size: 76 Copynumber: 4.7 Consensus size: 76
1139035 AGTCATCTTA
* * * * * *
1139045 CTTGAGAC-TGTTTTACTTGAAAGAAGATATTTCATTTGACTCAATATTGTTTTTCTCAAAACAA
1 CTTGAGACATGTTTTACTAGAAACAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAAAACAA
1139109 GATTTGTCTCG
66 GATTTGTCTCG
* * * *
1139120 CTTGAGACAGGTTTTATTAAAAACAAGACATTTCATTTCACTACATG-TTGTTTTTCTTAAAACA
1 CTTGAGACATGTTTTACTAGAAACAAGACATTTCATTTCACT-CAAGATTGTTTTTCTTAAAACA
*
1139184 A-CTTTCGTCTCG
65 AGATTT-GTCTCG
* * *
1139196 CTTGAGACATGTTTTATTAAAAACAAGACATTTCATTTCACTACATG-TTGTTTTTCTTAAAACA
1 CTTGAGACATGTTTTACTAGAAACAAGACATTTCATTTCACT-CAAGATTGTTTTTCTTAAAACA
*
1139260 A-CTTTCGTCTCG
65 AGATTT-GTCTCG
* * * *
1139272 CTTGAGACATTTTTTTACTCGAAATAAGAAGATTT-ATTTCACTCAAGATTGTTTTTCTTAAAAC
1 CTTGAGACA-TGTTTTACTAGAAACAAG-ACATTTCATTTCACTCAAGATTGTTTTTCTTAAAAC
1139336 AAGATTTGTCTCG
64 AAGATTTGTCTCG
* * * * *
1139349 CTTGAAACGATTTTTTACTCGAAAGAAGGCATTTCATTTCACTCAAGATTGTTTTT
1 CTTGAGAC-ATGTTTTACTAGAAACAAGACATTTCATTTCACTCAAGATTGTTTTT
1139405 AAAGAATATT
Statistics
Matches: 252, Mismatches: 24, Indels: 16
0.86 0.08 0.05
Matches are distributed among these distances:
75 11 0.04
76 140 0.56
77 92 0.37
78 9 0.04
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (76 bp):
CTTGAGACATGTTTTACTAGAAACAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAAAACAA
GATTTGTCTCG
Found at i:1139507 original size:40 final size:39
Alignment explanation
Indices: 1139407--1139508 Score: 125
Period size: 39 Copynumber: 2.6 Consensus size: 39
1139397 TTGTTTTTAA
* * *
1139407 AGAATATTTTATCTCGCTTGAGAAAGTTTCACTCGAATC
1 AGAAGATTTTATCTCGCTTGAGAAAGATTCACTCGAAAC
* * *
1139446 AGAAGATTTTATCTCGCTTGAGATAGATTCCCTCTAAAC
1 AGAAGATTTTATCTCGCTTGAGAAAGATTCACTCGAAAC
1139485 AGAAAGATTTTATCTC-CATTGAGA
1 AG-AAGATTTTATCTCGC-TTGAGA
1139509 CAATTTCCCT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 36 0.65
40 19 0.35
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGAAAGATTCACTCGAAAC
Found at i:1139517 original size:40 final size:38
Alignment explanation
Indices: 1139407--1139523 Score: 121
Period size: 39 Copynumber: 3.0 Consensus size: 38
1139397 TTGTTTTTAA
* * * *
1139407 AGAATATTTTATCTCGCTTGAGAAAGTTTCACTCGAATC
1 AGAAGATTTTATCTCGCTTGAGAAA-TTTCCCTCTAAAC
1139446 AGAAGATTTTATCTCGCTTGAGATAGA-TTCCCTCTAAAC
1 AGAAGATTTTATCTCGCTTGAGA-A-ATTTCCCTCTAAAC
*
1139485 AGAAAGATTTTATCTC-CATTGAGACAATTTCCCTTTAAA
1 AG-AAGATTTTATCTCGC-TTGAGA-AATTTCCCTCTAAA
1139524 AAAATTTTGT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
39 35 0.52
40 31 0.46
41 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (38 bp):
AGAAGATTTTATCTCGCTTGAGAAATTTCCCTCTAAAC
Found at i:1139540 original size:21 final size:21
Alignment explanation
Indices: 1139514--1139599 Score: 85
Period size: 21 Copynumber: 4.4 Consensus size: 21
1139504 TGAGACAATT
*
1139514 TCCCTTTAAAAAAATTTTGTC
1 TCCCTTGAAAAAAATTTTGTC
*
1139535 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAAAAAATTTTGTC
* *
1139556 TCCCTTG-AGACAA---T-T-
1 TCCCTTGAAAAAAATTTTGTC
*
1139571 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAAAAAATTTTGTC
1139592 TCCCTTGA
1 TCCCTTGA
1139600 GACAGTTTCC
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
15 7 0.14
16 4 0.08
17 1 0.02
19 1 0.02
20 4 0.08
21 34 0.67
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.38
Consensus pattern (21 bp):
TCCCTTGAAAAAAATTTTGTC
Found at i:1139566 original size:57 final size:57
Alignment explanation
Indices: 1139491--1139599 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
1139481 AAACAGAAAG
*
1139491 ATTTTATCTCCATTGAGACAATTTCCCTTTAAAAAAATTTTGTCTCCCTTGAAACAA
1 ATTTTATCTCCATTGAGACAATTTCCCTTGAAAAAAATTTTGTCTCCCTTGAAACAA
* * *
1139548 ATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGA
1 ATTTTATCTCCATTGAGACAATTTCCCTTGAAAAAAATTTTGTCTCCCTTGA
1139600 GACAGTTTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.39
Consensus pattern (57 bp):
ATTTTATCTCCATTGAGACAATTTCCCTTGAAAAAAATTTTGTCTCCCTTGAAACAA
Found at i:1139575 original size:36 final size:36
Alignment explanation
Indices: 1139535--1139726 Score: 330
Period size: 36 Copynumber: 5.3 Consensus size: 36
1139525 AAATTTTGTC
*
1139535 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
1139571 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
*
1139607 TCCTTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
*
1139643 TCCCTTGAAACAAATTTTGTCTTCCTTGAGACAGTT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
* *
1139679 CCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
*
1139715 TCACTTGAAACA
1 TCCCTTGAAACA
1139727 GAAGATTTTA
Statistics
Matches: 147, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 147 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (36 bp):
TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
Found at i:1139847 original size:43 final size:43
Alignment explanation
Indices: 1139796--1140026 Score: 324
Period size: 43 Copynumber: 5.4 Consensus size: 43
1139786 CCTGATTTTC
* *
1139796 AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
* * *
1139839 AGAGGTTTCTTGATGAAAAGCTTGAGGGACCGTCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
* *
1139882 AGGGGTTCCTTGATGACAAGCTTGA-AGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGA-GACCATCGTGATATGT
*
1139925 AGGGG-TTCTTTGA-GAACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTC-TTGATGAA-AAGCTTGAGAGACCATCGTGATATGT
*
1139968 AGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
*
1140011 AGGGGTTCCTTGATGA
1 AGGGGTTTCTTGATGA
1140027 CAAATTTGAT
Statistics
Matches: 166, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
42 4 0.02
43 155 0.93
44 7 0.04
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (43 bp):
AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
Found at i:1139975 original size:129 final size:129
Alignment explanation
Indices: 1139796--1140029 Score: 418
Period size: 129 Copynumber: 1.8 Consensus size: 129
1139786 CCTGATTTTC
1139796 AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGAGGTTTCTTGATGAAAAGCT
1 AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGAGGTTTCTTGATGAAAAGCT
*
1139861 TGAGGGACCGTCGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
66 TGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
*
1139925 AGGGG-TTCTTTG-AGAACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAG
1 AGGGGTTTC-TTGAAGAA-AAGCTTGAGAAACCATCGTGATATGTAGAGGTTTCTTGATGAAAAG
1139988 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAA
64 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAA
1140030 ATTTGATGAC
Statistics
Matches: 101, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
128 7 0.07
129 94 0.93
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.29
Consensus pattern (129 bp):
AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGAGGTTTCTTGATGAAAAGCT
TGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
Found at i:1140331 original size:35 final size:33
Alignment explanation
Indices: 1140235--1140318 Score: 134
Period size: 35 Copynumber: 2.5 Consensus size: 33
1140225 AATAAGAAGG
*
1140235 TCAAACCATTAACC-AAAAACAACCTGAGACAT
1 TCAAACCATTGACCAAAAAACAACCTGAGACAT
1140267 TCAAACCATTGACCAAAAATAGCAACCTGAGACAT
1 TCAAACCATTGACCAAAAA-A-CAACCTGAGACAT
1140302 TCAAACCATTGACCAAA
1 TCAAACCATTGACCAAA
1140319 CACAATAACC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
32 13 0.27
33 4 0.08
34 1 0.02
35 30 0.62
ACGTcount: A:0.48, C:0.27, G:0.08, T:0.17
Consensus pattern (33 bp):
TCAAACCATTGACCAAAAAACAACCTGAGACAT
Found at i:1140698 original size:32 final size:32
Alignment explanation
Indices: 1140657--1140790 Score: 216
Period size: 32 Copynumber: 4.2 Consensus size: 32
1140647 AAACAATAAA
1140657 GGGCATCTTTGAAGATTCAACATCAAATATTG
1 GGGCATCTTTGAAGATTCAACATCAAATATTG
1140689 GGGCATCTTTGAAGATTCAACATCAAATATTG
1 GGGCATCTTTGAAGATTCAACATCAAATATTG
*
1140721 GGGCATCTTT-AGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGA-AGATTCAACATCAAATATTG
* * *
1140753 GGGCATCTTTGGAGATTCAATATCGAATATTG
1 GGGCATCTTTGAAGATTCAACATCAAATATTG
1140785 GGGCAT
1 GGGCAT
1140791 TCAATATCCT
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
31 1 0.01
32 94 0.99
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (32 bp):
GGGCATCTTTGAAGATTCAACATCAAATATTG
Found at i:1140943 original size:34 final size:34
Alignment explanation
Indices: 1140904--1141018 Score: 203
Period size: 34 Copynumber: 3.4 Consensus size: 34
1140894 AATTGTCTCA
*
1140904 CTTGAGATAATTTCTCAAAACAAATTTCGTCTTG
1 CTTGAGACAATTTCTCAAAACAAATTTCGTCTTG
* *
1140938 CTTGAGACAATTTCTCAAAAAAAAATTCGTCTTG
1 CTTGAGACAATTTCTCAAAACAAATTTCGTCTTG
1140972 CTTGAGACAATTTCTCAAAACAAATTTCGTCTTG
1 CTTGAGACAATTTCTCAAAACAAATTTCGTCTTG
1141006 CTTGAGACAATTT
1 CTTGAGACAATTT
1141019 TTCTCTGAGA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 76 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (34 bp):
CTTGAGACAATTTCTCAAAACAAATTTCGTCTTG
Found at i:1140976 original size:68 final size:67
Alignment explanation
Indices: 1140888--1141018 Score: 226
Period size: 68 Copynumber: 1.9 Consensus size: 67
1140878 GTTTCTCTTT
*
1140888 AAAAAAAATTGTCTCACTTGAGATAATTTCTCAAAACAAATTTCGTCTTGCTTGAGACAATTTCT
1 AAAAAAAATTGTCTCACTTGAGACAATTTCTCAAAACAAATTTCGTCTTGCTTGAGACAATTTCT
1140953 CA
66 CA
**
1140955 AAAAAAAATTCGTCTTGCTTGAGACAATTTCTCAAAACAAATTTCGTCTTGCTTGAGACAATTT
1 AAAAAAAATT-GTCTCACTTGAGACAATTTCTCAAAACAAATTTCGTCTTGCTTGAGACAATTT
1141019 TTCTCTGAGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
67 10 0.17
68 50 0.83
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (67 bp):
AAAAAAAATTGTCTCACTTGAGACAATTTCTCAAAACAAATTTCGTCTTGCTTGAGACAATTTCT
CA
Found at i:1141303 original size:76 final size:76
Alignment explanation
Indices: 1141195--1141479 Score: 321
Period size: 76 Copynumber: 3.8 Consensus size: 76
1141185 AACAAAGTCA
* ** * *
1141195 TCTCACTTGAGAC-GGTTTTACTTGAAAGAAGACATTTCATTTGACTCAAGATTGTTTTTCTCAA
1 TCTCGCTTGAGACAGGTTTTACTCAAAAGAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAA
1141259 AACAAGATTTG
66 AACAAGATTTG
* * * *
1141270 TCTCGCTTGAGACAGGTTTTATTCAAAACAAGACATTTTATTTCACT--ACA-TGTTTTTCTTAA
1 TCTCGCTTGAGACAGGTTTTACTCAAAAGAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAA
*
1141332 AACAA-CTTTCG
66 AACAAGATTT-G
** * * * *
1141343 TCTCGCTTGAGACATTTTTTACTCGAAATAAGA-AGATTCATTTCACTCAAGATTATTTTTCTTA
1 TCTCGCTTGAGACAGGTTTTACTCAAAAGAAGACA-TTTCATTTCACTCAAGATTGTTTTTCTTA
1141407 AAACAAGATTTG
65 AAACAAGATTTG
** * *
1141419 TCTCGCTTGAGACGATTTTTTACTCAAAAGAAGGCATTTCATTTCACTCAATATTGTTTTT
1 TCTCGCTTGAGAC-AGGTTTTACTCAAAAGAAGACATTTCATTTCACTCAAGATTGTTTTT
1141480 AAAGAAGATT
Statistics
Matches: 175, Mismatches: 26, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
72 4 0.02
73 55 0.31
74 2 0.01
75 14 0.08
76 57 0.33
77 42 0.24
78 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (76 bp):
TCTCGCTTGAGACAGGTTTTACTCAAAAGAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAA
AACAAGATTTG
Found at i:1141336 original size:73 final size:75
Alignment explanation
Indices: 1141195--1141504 Score: 278
Period size: 73 Copynumber: 4.2 Consensus size: 75
1141185 AACAAAGTCA
* ** * * * *
1141195 TCTCACTTGAGAC-GGTTTTACTTGAAAGAAGACATTTCATTTGACTCAAGATTGTTTTTCTCAA
1 TCTCGCTTGAGACAGGTTTTACTCAAAAGAAGACATTTCATTTCACT-AACATTATTTTTCTTAA
1141259 AACAAGATTTG
65 AACAAGATTTG
* * * *
1141270 TCTCGCTTGAGACAGGTTTTATTCAAAACAAGACATTTTATTTCACT-ACA-TGTTTTTCTTAAA
1 TCTCGCTTGAGACAGGTTTTACTCAAAAGAAGACATTTCATTTCACTAACATTATTTTTCTTAAA
*
1141333 ACAA-CTTTCG
66 ACAAGATTT-G
** * * * *
1141343 TCTCGCTTGAGACATTTTTTACTCGAAATAAGA-AGATTCATTTCACTCAAGATTATTTTTCTTA
1 TCTCGCTTGAGACAGGTTTTACTCAAAAGAAGACA-TTTCATTTCACT-AACATTATTTTTCTTA
1141407 AAACAAGATTTG
64 AAACAAGATTTG
** * *
1141419 TCTCGCTTGAGACGATTTTTTACTCAAAAGAAGGCATTTCATTTCACT--CAATATTGTTT-TT-
1 TCTCGCTTGAGAC-AGGTTTTACTCAAAAGAAGACATTTCATTTCACTAACATTATT-TTTCTTA
* *
1141480 AAAGAAGATTCTA
64 AAACAAGATT-TG
1141493 TCTCGCTTGAGA
1 TCTCGCTTGAGA
1141505 AAGTTTCCCT
Statistics
Matches: 196, Mismatches: 28, Indels: 23
0.79 0.11 0.09
Matches are distributed among these distances:
72 4 0.02
73 64 0.33
74 22 0.11
75 17 0.09
76 57 0.29
77 31 0.16
78 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (75 bp):
TCTCGCTTGAGACAGGTTTTACTCAAAAGAAGACATTTCATTTCACTAACATTATTTTTCTTAAA
ACAAGATTTG
Found at i:1141517 original size:149 final size:149
Alignment explanation
Indices: 1141230--1141518 Score: 352
Period size: 149 Copynumber: 1.9 Consensus size: 149
1141220 AAGAAGACAT
* * *
1141230 TTCATTTGACTCAAGATTGTTTTTCTCAAAACAAGATTTGTCTCGCTTGAGACAGGTTTTATTCA
1 TTCATTTCACTCAAGATTATTTTTCTCAAAACAAGATTTGTCTCGCTTGAGACAGGTTTTACTCA
* * * * **
1141295 AAACAAGACATTTTATTTCACTACATGTTTTTCTTAAAACAACTTTCGTCTCGCTTGAGACATTT
66 AAACAAGACATTTCATTTCACTACATATTTTTCTTAAAACAACATTCATCTCGCTTGAGACAAGT
*
1141360 TTTACTCGAAATAAGAAGA
131 TTCACTCGAAATAAGAAGA
* **
1141379 TTCATTTCACTCAAGATTATTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACGATTTTTTACTC
1 TTCATTTCACTCAAGATTATTTTTCTCAAAACAAGATTTGTCTCGCTTGAGAC-AGGTTTTACTC
* * * *
1141444 AAAAGAAGGCATTTCATTTCACT-CAATATTGTTT-TT-AAAGAAGATTCTATCTCGCTTGAGA-
65 AAAACAAGACATTTCATTTCACTAC-ATATT-TTTCTTAAAACAACATTC-ATCTCGCTTGAGAC
*
1141505 AAGTTTCCCTCGAA
127 AAGTTTCACTCGAA
1141519 GCAGAAGATT
Statistics
Matches: 118, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
149 69 0.58
150 46 0.39
151 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (149 bp):
TTCATTTCACTCAAGATTATTTTTCTCAAAACAAGATTTGTCTCGCTTGAGACAGGTTTTACTCA
AAACAAGACATTTCATTTCACTACATATTTTTCTTAAAACAACATTCATCTCGCTTGAGACAAGT
TTCACTCGAAATAAGAAGA
Found at i:1141613 original size:21 final size:21
Alignment explanation
Indices: 1141584--1141652 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 21
1141574 TCACTTGAGA
*
1141584 TAGTTTCCCTTGAAACAAATT
1 TAGTCTCCCTTGAAACAAATT
*
1141605 TAGTCTCCCTTGAGAC-----
1 TAGTCTCCCTTGAAACAAATT
*
1141621 -AGTTTCCCTTGAAACAAATT
1 TAGTCTCCCTTGAAACAAATT
*
1141641 TTGTCTCCCTTG
1 TAGTCTCCCTTG
1141653 GGACAGTTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
15 13 0.36
21 23 0.64
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.38
Consensus pattern (21 bp):
TAGTCTCCCTTGAAACAAATT
Found at i:1141625 original size:36 final size:36
Alignment explanation
Indices: 1141493--1141853 Score: 463
Period size: 36 Copynumber: 9.8 Consensus size: 36
1141483 GAAGATTCTA
* * * * *
1141493 TCTCGCTTGAGAAAGTTTCCCTCGAAGCAGAAGATTTTA
1 TCTCCCTTGAGACAGTTTCCCTTGAA--ACAA-ATTTTG
* * ** *
1141532 TCTCGCTTGAGATAGTTTCCCTCAAAACAGAAAGATTTTA
1 TCTCCCTTGAGACAGTTTCCCTTGAAAC---AA-ATTTTG
* * *
1141572 TCTCACTTGAGATAGTTTCCCTTGAAACAAATTTAG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1141608 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG
*
1141644 TCTCCCTTGGGACAGTTTCCCTTGAAACAAATTTTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG
* *
1141680 TCTCCCTTGAGATAGTTTCCTTTGAAACAAATTTTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1141716 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1141752 TCTCCCTTGAGAC-GATTTCCCTTGAAACAAATTTTG
1 TCTCCCTTGAGACAG-TTTCCCTTGAAACAAATTTTG
* *
1141788 TCTTCCTTGAGACAGTTCCCCTTGAAACAAATTTTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG
* *
1141824 TCTCCCTTGAGACAGTCTCCCTTGAGACAA
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAA
1141854 TTTCACTTGA
Statistics
Matches: 294, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
35 1 0.00
36 231 0.79
37 4 0.01
39 24 0.08
40 34 0.12
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (36 bp):
TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG
Found at i:1141843 original size:15 final size:15
Alignment explanation
Indices: 1141823--1141852 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1141813 AACAAATTTT
1141823 GTCTCCCTTGAGACA
1 GTCTCCCTTGAGACA
1141838 GTCTCCCTTGAGACA
1 GTCTCCCTTGAGACA
1141853 ATTTCACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (15 bp):
GTCTCCCTTGAGACA
Found at i:1141905 original size:39 final size:39
Alignment explanation
Indices: 1141839--1141915 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 39
1141829 CTTGAGACAG
* *
1141839 TCTCCCTTGAGACAATTTCACTTGAAACAGAAGATTTTA
1 TCTCCCTTGAGACAATTTCACTCGAAACACAAGATTTTA
* * * * *
1141878 TCTCGCTTGAGATAGTTTCGCTCGAAACACAATATTTT
1 TCTCCCTTGAGACAATTTCACTCGAAACACAAGATTTT
1141916 TAGAAACTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (39 bp):
TCTCCCTTGAGACAATTTCACTCGAAACACAAGATTTTA
Found at i:1142003 original size:43 final size:43
Alignment explanation
Indices: 1141948--1142280 Score: 202
Period size: 43 Copynumber: 7.2 Consensus size: 43
1141938 GGGGTTTTTT
* *
1141948 TTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTA
1 TTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTA
* * * *
1141991 TTGATGAAAAGCTTGAGGGACCGTTGTGATATGTAGGAGTTCCTTGATGACAAA
1 TTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGG-G---GTT--T-----A
* * *
1142045 TTTGATGACAAGCTTGA-AGGATCACCGTGATATGTAGGGGTTCT-
1 -TTGATGAAAAGCTTGAGA-GACCATCGTGATATGTAGGGGTT-TA
* * * * *
1142089 TTAAGGACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTC
1 TTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTA
*
1142132 TTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGGTTCCTTGATGACAAA
1 TTGATGAAAAGCTTGAGAGACCATCGTGATATGTA-GGGG----TT--T-----A
* * * * *
1142187 TTTGATGACAAGCTTGAGAAACCATCGTGATATGTTGGAGTTTC
1 -TTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTA
* **
1142231 TTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTCC
1 TTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTA
1142274 TTGATGA
1 TTGATGA
1142281 CAAATTTGAT
Statistics
Matches: 225, Mismatches: 37, Indels: 56
0.71 0.12 0.18
Matches are distributed among these distances:
42 1 0.00
43 140 0.62
44 6 0.03
47 2 0.01
48 2 0.01
49 2 0.01
50 2 0.01
51 4 0.02
54 2 0.01
55 33 0.15
56 31 0.14
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (43 bp):
TTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTA
Found at i:1142212 original size:99 final size:98
Alignment explanation
Indices: 1142094--1142330 Score: 388
Period size: 99 Copynumber: 2.4 Consensus size: 98
1142084 GTTCTTTAAG
1142094 GACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGT
1 GACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGT
1142159 GATATGTAGGGGGTTCCTTGATGACAAATTTGAT
66 GATATGTA-GGGGTTCCTTGATGACAAATTTGAT
* *
1142193 GACAAGCTTGAGAAACCATCGTGATATGTTGGAGTTTCTTGATGAAAAGCTTGAGGGACCATCGT
1 GACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGT
1142258 GATATGTAGGGGTTCCTTGATGACAAATTTGAT
66 GATATGTAGGGGTTCCTTGATGACAAATTTGAT
** * *
1142291 GA-ACA-CTTGAGGGACCAACGTGATATGTAGGGGTTCCTTG
1 GACA-AGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTG
1142331 GTGACAATTT
Statistics
Matches: 129, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
97 30 0.23
98 28 0.22
99 71 0.55
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (98 bp):
GACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGT
GATATGTAGGGGTTCCTTGATGACAAATTTGAT
Found at i:1142265 original size:142 final size:141
Alignment explanation
Indices: 1141947--1142280 Score: 485
Period size: 142 Copynumber: 2.4 Consensus size: 141
1141937 AGGGGTTTTT
*
1141947 TTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTATTGATGAAAAGCTTGAGGGAC
1 TTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGAC
* * * *
1142012 CGTTGTGATATGTAGGAGTTCCTTGATGACAAATTTGATGACAAGCTTGAAGGATCACCGTGATA
66 CATCGTGATATGTAGGAGTTCCTTGATGACAAATTTGATGACAAGCTTGAAGAACCACCGTGATA
1142077 TGTAGGGGTTC
131 TGTAGGGGTTC
*
1142088 TTT-AAGGACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGA
1 TTTGAA-GAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGA
* *
1142152 CCATCGTGATATGTAGGGGGTTCCTTGATGACAAATTTGATGACAAGCTTG-AGAAACCATCGTG
65 CCATCGTGATATGTA-GGAGTTCCTTGATGACAAATTTGATGACAAGCTTGAAG-AACCACCGTG
* *
1142216 ATATGTTGGAGTT-
128 ATATGTAGGGGTTC
* ** *
1142229 TCTTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGA
1 T-TTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGA
1142281 CAAATTTGAT
Statistics
Matches: 173, Mismatches: 15, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
140 2 0.01
141 75 0.43
142 95 0.55
143 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (141 bp):
TTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGAC
CATCGTGATATGTAGGAGTTCCTTGATGACAAATTTGATGACAAGCTTGAAGAACCACCGTGATA
TGTAGGGGTTC
Found at i:1142314 original size:54 final size:55
Alignment explanation
Indices: 1142231--1142337 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 55
1142221 TTGGAGTTTC
*
1142231 TTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAAT
1 TTGATGAAAAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAAT
* *
1142286 TTGATGAACA-CTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGGTGACAA
1 TTGATGAAAAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAA
1142338 TTTAGAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 40 0.82
55 9 0.18
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (55 bp):
TTGATGAAAAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAAAT
Found at i:1144216 original size:2 final size:2
Alignment explanation
Indices: 1144209--1144266 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1144199 ATTACTGTTA
1144209 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
1144251 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1144267 TGTTTGTCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1147738 original size:15 final size:15
Alignment explanation
Indices: 1147718--1147752 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1147708 GCTGTCAAAC
1147718 ATAAATTATATCATA
1 ATAAATTATATCATA
*
1147733 ATAAATTATATTATA
1 ATAAATTATATCATA
1147748 ATAAA
1 ATAAA
1147753 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATTATATCATA
Found at i:1148222 original size:26 final size:25
Alignment explanation
Indices: 1148172--1148221 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1148162 TATTTATTAA
*
1148172 ATATTTCAATAATTGTTTATATTTT
1 ATATTTAAATAATTGTTTATATTTT
*
1148197 ATATTTAAATTAATTTTTTA-ATTTT
1 ATATTTAAA-TAATTGTTTATATTTT
1148222 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
ATATTTAAATAATTGTTTATATTTT
Found at i:1151298 original size:48 final size:47
Alignment explanation
Indices: 1151211--1151302 Score: 109
Period size: 48 Copynumber: 1.9 Consensus size: 47
1151201 ATAAAAGATT
* *
1151211 TCGTCATGTGAAGTTGAGTTTTAAAAATAATAATTTTTTTATTTAAAC
1 TCGTCATGTGAAATTGAGTTTTAAAAATAATAATATTTTT-TTTAAAC
1151259 TCGTCATGTGAAATAATGA-TTTCTAAAAAT-AT-ATATTTTTTTTA
1 TCGTCATGTGAAAT--TGAGTTT-TAAAAATAATAATATTTTTTTTA
1151303 TTAAAATCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
47 4 0.10
48 20 0.51
49 5 0.13
50 10 0.26
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (47 bp):
TCGTCATGTGAAATTGAGTTTTAAAAATAATAATATTTTTTTTAAAC
Found at i:1152471 original size:34 final size:35
Alignment explanation
Indices: 1152385--1152627 Score: 179
Period size: 34 Copynumber: 6.9 Consensus size: 35
1152375 ATATATAGTT
1152385 TTTTG-AAAACT-TATATAATATATAGTTTTTAAAAACA
1 TTTTGAAAAACTATATAT-A-ATATAG-TTTT-AAAACA
*
1152422 TTTT-AAAAAC-GTATATAATATAGTTTTAAAACA
1 TTTTGAAAAACTATATATAATATAGTTTTAAAACA
* * *
1152455 -TTTGAAAACCTATATAT-ACATAGTTTTTGAAACA
1 TTTTGAAAAACTATATATAATATAG-TTTTAAAACA
1152489 TTTTTG-AAAAC-ATATATAATATAGTTTTAAAAACA
1 -TTTTGAAAAACTATATATAATATAGTTTT-AAAACA
* * *
1152524 TTTTTAAAAAATATATATAATATATAGTTTTAAAAATA
1 TTTTGAAAAACTATATAT-A-ATATAGTTTT-AAAACA
* * * *
1152562 TTTTTGAAAAAATATATATTATATATTTTTGAAAATA
1 -TTTTGAAAAACTATATATAATATAGTTTT-AAAACA
1152599 TTTTTG--AAA-TATAT-T-ATATAGTTTTAAAA
1 -TTTTGAAAAACTATATATAATATAGTTTTAAAA
1152628 AAATATTTTG
Statistics
Matches: 177, Mismatches: 15, Indels: 34
0.78 0.07 0.15
Matches are distributed among these distances:
31 4 0.02
32 12 0.07
33 17 0.10
34 37 0.21
35 27 0.15
36 11 0.06
37 36 0.20
38 16 0.09
39 17 0.10
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
TTTTGAAAAACTATATATAATATAGTTTTAAAACA
Found at i:1152506 original size:68 final size:70
Alignment explanation
Indices: 1152386--1152584 Score: 210
Period size: 68 Copynumber: 2.8 Consensus size: 70
1152376 TATATAGTTT
* * *
1152386 TTTGAAAACTTATATAATATATAGTTTTTAAAAACATTTTAAAAACGTATATAATATAGTTTT-A
1 TTTGAAAACCTATATAATACATAGTTTTTAAAAACATTTTAAAAACATATATAATATAGTTTTAA
1152450 AAACA
66 AAACA
* *
1152455 TTTGAAAACCTATAT-ATACATAGTTTTT-GAAACATTTTTGAAAACATATATAATATAGTTTTA
1 TTTGAAAACCTATATAATACATAGTTTTTAAAAACA-TTTTAAAAACATATATAATATAGTTTTA
1152518 AAAACA
65 AAAACA
* ** * * *
1152524 TTTTTAAAAAATATATATAATATATAG-TTTTAAAAATATTTTTGAAAAA-ATATATATTATA
1 --TTT-GAAAACCTATATAATACATAGTTTTTAAAAACA-TTTT-AAAAACATATATAATATA
1152585 TATTTTTGAA
Statistics
Matches: 109, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
67 5 0.05
68 37 0.34
69 20 0.18
71 3 0.03
72 13 0.12
73 27 0.25
74 4 0.04
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (70 bp):
TTTGAAAACCTATATAATACATAGTTTTTAAAAACATTTTAAAAACATATATAATATAGTTTTAA
AAACA
Found at i:1152603 original size:37 final size:36
Alignment explanation
Indices: 1152384--1152637 Score: 233
Period size: 37 Copynumber: 7.2 Consensus size: 36
1152374 AATATATAGT
**
1152384 TTTTTGAAAACTTATATAATATATAGTTTTTAAAAACA
1 TTTTTGAAAAAATATAT-ATATATAG-TTTTAAAAACA
*
1152422 -TTTT-AAAAACGTATATA-ATATAGTTTT-AAAACA
1 TTTTTGAAAAA-ATATATATATATAGTTTTAAAAACA
** * **
1152455 --TTTGAAAACCTATATATACATAGTTTTTGAAACA
1 TTTTTGAAAAAATATATATATATAGTTTTAAAAACA
*
1152489 TTTTTGAAAACATATATA-ATATAGTTTTAAAAACA
1 TTTTTGAAAAAATATATATATATAGTTTTAAAAACA
* *
1152524 TTTTTAAAAAATATATATAATATATAGTTTTAAAAATA
1 TTTTTGAAAAA-ATATAT-ATATATAGTTTTAAAAACA
* * *
1152562 TTTTTGAAAAAATATATATTATATATTTTTGAAAATA
1 TTTTTGAAAAAATATATA-TATATAGTTTTAAAAACA
*
1152599 TTTTTG---AAATATAT-TATATAGTTTTAAAAAAA
1 TTTTTGAAAAAATATATATATATAGTTTTAAAAACA
1152631 TATTTTG
1 T-TTTTG
1152638 GGAAATATTT
Statistics
Matches: 186, Mismatches: 19, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
32 25 0.13
33 24 0.13
34 17 0.09
35 29 0.16
36 27 0.15
37 38 0.20
38 26 0.14
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
TTTTTGAAAAAATATATATATATAGTTTTAAAAACA
Found at i:1152666 original size:23 final size:23
Alignment explanation
Indices: 1152640--1152700 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
1152630 ATATTTTGGG
*
1152640 AAATATTTTGAAAACATTTTAAA
1 AAATATTTTGAAAACAATTTAAA
1152663 AAATA-TTT-AATATACAATTTAAA
1 AAATATTTTGAA-A-ACAATTTAAA
1152686 AAATATTTTCGAAAA
1 AAATATTTT-GAAAA
1152701 TATATGATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
21 2 0.06
22 4 0.12
23 19 0.59
24 4 0.12
25 1 0.03
26 2 0.06
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (23 bp):
AAATATTTTGAAAACAATTTAAA
Found at i:1152774 original size:16 final size:16
Alignment explanation
Indices: 1152753--1152793 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1152743 TTTTCATTAC
*
1152753 ATTTTATTTCTTTTTT
1 ATTTTATTTCTTCTTT
1152769 CA-TTTATTTCTTCTTT
1 -ATTTTATTTCTTCTTT
1152785 ATTTTATTT
1 ATTTTATTT
1152794 ATTTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTATTTCTTCTTT
Found at i:1152795 original size:20 final size:19
Alignment explanation
Indices: 1152760--1152797 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1152750 TACATTTTAT
1152760 TTCTTTTTTCATTTATTTC
1 TTCTTTTTTCATTTATTTC
*
1152779 TTCTTTATTTTATTTATTT
1 TTCTTT-TTTCATTTATTT
1152798 ATTTTTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (19 bp):
TTCTTTTTTCATTTATTTC
Found at i:1152814 original size:20 final size:22
Alignment explanation
Indices: 1152760--1152814 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
1152750 TACATTTTAT
*
1152760 TTCTTTTTTCATTTATTTCTTC
1 TTCTTTTTTTATTTATTTCTTC
*
1152782 TTTATTTTATTTATTTATTT-TTC
1 -TTCTTTT-TTTATTTATTTCTTC
1152805 -TCTTTTTTTA
1 TTCTTTTTTTA
1152815 GGGTCCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 5 0.18
23 9 0.32
24 10 0.36
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (22 bp):
TTCTTTTTTTATTTATTTCTTC
Found at i:1155539 original size:14 final size:14
Alignment explanation
Indices: 1155515--1155562 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1155505 CACTAACTTT
1155515 TTTTGTTTCCTTTCA
1 TTTT-TTTCCTTTCA
1155530 TTTTTTTCCTTTC-
1 TTTTTTTCCTTTCA
*
1155543 TTTATTTT-ATTTCA
1 TTT-TTTTCCTTTCA
1155557 TTTTTT
1 TTTTTT
1155563 ATCATTACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 10 0.33
14 16 0.53
15 4 0.13
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTTTTCCTTTCA
Found at i:1159720 original size:2 final size:2
Alignment explanation
Indices: 1159713--1159745 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1159703 TCATATTCTT
1159713 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 T
1159746 TAACTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1159782 original size:24 final size:24
Alignment explanation
Indices: 1159732--1159853 Score: 64
Period size: 24 Copynumber: 4.7 Consensus size: 24
1159722 ATATATATAT
* *
1159732 ATATATATATATATTAACTTAAAAA
1 ATATAT-TTTATATTAAATTAAAAA
* * **
1159757 ATGTTTTTTATATTAAATTATTAA
1 ATATATTTTATATTAAATTAAAAA
*
1159781 ATATATTTTATTATTAATTTAATTTAAA
1 ATATATTTTA-TATTAAATTAA---AAA
* * *
1159809 ATATATGTCTTTATTTTTATTTAAAAA
1 ATATA--T-TTTATATTAAATTAAAAA
*
1159836 TATATATTTTATGTTAAA
1 -ATATATTTTATATTAAA
1159854 AGTTGTTTAA
Statistics
Matches: 73, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
24 22 0.30
25 21 0.29
26 1 0.01
27 3 0.04
28 12 0.16
30 10 0.14
31 4 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
ATATATTTTATATTAAATTAAAAA
Found at i:1160041 original size:31 final size:31
Alignment explanation
Indices: 1159976--1160045 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
1159966 CATGATGACC
* *
1159976 ATATCTTAATTAAATAAAAACGAAAGTCACT
1 ATATCTTAATTAAATAAAAACAAAAATCACT
* * * *
1160007 ATATCTTTATTAAATAAAAATAAAAATGATT
1 ATATCTTAATTAAATAAAAACAAAAATCACT
1160038 ATATCTTA
1 ATATCTTA
1160046 TGTTTTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (31 bp):
ATATCTTAATTAAATAAAAACAAAAATCACT
Found at i:1161578 original size:2 final size:2
Alignment explanation
Indices: 1161571--1161596 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1161561 CTCCGTATTA
1161571 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
1161597 TTGCTTGTAT
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:1165531 original size:154 final size:152
Alignment explanation
Indices: 1165246--1165551 Score: 569
Period size: 154 Copynumber: 2.0 Consensus size: 152
1165236 TATTGCGATC
1165246 AGGATAGGTGCTTTCGTAAATAAAATAGCAACAAATTATATGATCTTAAGCAGAAGATGAGGAAA
1 AGGATAGGTGCTTTCGTAAATAAAATAGCAACAAATTATATGATCTTAAGCAGAAGATGAGGAAA
1165311 ACTGACACGGTTTCCCTATTGACCAGTAATTTTAAGACATGGGAAAAATGTAGCTTGAAAAAAAA
66 ACTGACACGGTTTCCCTATTGACCAGTAATTTTAAGACATGGGAAAAATGTAGCTTGAAAAAAAA
1165376 AATTACCGGCTGAGATACTTCA
131 AATTACCGGCTGAGATACTTCA
1165398 AGGATAGGTGCTTTCGTAAATAAAATAGCAACAAATTATATTGATCTTTAAGCAGAAGATGAGGA
1 AGGATAGGTGCTTTCGTAAATAAAATAGCAACAAATTATA-TGATC-TTAAGCAGAAGATGAGGA
*
1165463 AAACTGACACGGTTTCCCTATTGACCAGTAAATTTTAAGACATGGGAAAAATGTAGCTTG-AAAG
64 AAACTGACACGGTTTCCCTATTGACCAGT-AATTTTAAGACATGGGAAAAATGTAGCTTGAAAAA
1165527 AAAAATTACCGGCTGAGATACTTCA
128 AAAAATTACCGGCTGAGATACTTCA
1165552 TTCTCCGATC
Statistics
Matches: 150, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
152 40 0.27
153 5 0.03
154 75 0.50
155 30 0.20
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (152 bp):
AGGATAGGTGCTTTCGTAAATAAAATAGCAACAAATTATATGATCTTAAGCAGAAGATGAGGAAA
ACTGACACGGTTTCCCTATTGACCAGTAATTTTAAGACATGGGAAAAATGTAGCTTGAAAAAAAA
AATTACCGGCTGAGATACTTCA
Found at i:1173140 original size:26 final size:27
Alignment explanation
Indices: 1173090--1173147 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
1173080 ATCAATTATA
*
1173090 ATATATTAATAGATATATATATAAAGT
1 ATATATTAATAGATATATATATAAACT
*
1173117 ATATATTAATATA-ATATATATAAACT
1 ATATATTAATAGATATATATATAAACT
1173143 ATATA
1 ATATA
1173148 ATTTGTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 17 0.59
27 12 0.41
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (27 bp):
ATATATTAATAGATATATATATAAACT
Found at i:1173148 original size:18 final size:18
Alignment explanation
Indices: 1173125--1173346 Score: 51
Period size: 18 Copynumber: 11.7 Consensus size: 18
1173115 GTATATATTA
1173125 ATATAATATATATAAACT
1 ATATAATATATATAAACT
* * *
1173143 ATATAATTTGTATTTATAATT
1 ATATAA--TATATATA-AACT
* * *
1173164 TTATATATGTATATAAACC
1 ATATA-ATATATATAAACT
**
1173183 ATGCAATATATATATATA-T
1 ATATAATATATATA-A-ACT
*
1173202 ATATATATATATATTAA-T
1 ATATA-ATATATATAAACT
* *
1173220 A-AAACATATATATATA-T
1 ATATA-ATATATATAAACT
*
1173237 ATATATATATATATTGCACAGCTT
1 ATATA-ATATATA-T--A-AAC-T
* *
1173261 ATATAATTTATAT-AATT
1 ATATAATATATATAAACT
* *
1173278 ATACTAATAAACTATATAATT
1 ATA-TAATATA-TATA-AACT
*
1173299 CAT-TAGTATATATAAACT
1 -ATATAATATATATAAACT
** *
1173317 ATATGGTATATATAAATT
1 ATATAATATATATAAACT
*
1173335 ATATATTATATA
1 ATATAATATATA
1173347 GTTCATTATT
Statistics
Matches: 149, Mismatches: 35, Indels: 40
0.67 0.16 0.18
Matches are distributed among these distances:
17 19 0.13
18 58 0.39
19 17 0.11
20 27 0.18
21 12 0.08
22 4 0.03
23 6 0.04
24 6 0.04
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (18 bp):
ATATAATATATATAAACT
Found at i:1173265 original size:2 final size:2
Alignment explanation
Indices: 1173188--1173250 Score: 87
Period size: 2 Copynumber: 33.0 Consensus size: 2
1173178 AAACCATGCA
* *
1173188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT A- AA AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1173227 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
1173251 TGCACAGCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 53 0.95
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1173328 original size:33 final size:33
Alignment explanation
Indices: 1173290--1173454 Score: 110
Period size: 33 Copynumber: 5.1 Consensus size: 33
1173280 ACTAATAAAC
*
1173290 TATATAATTCATTAGTATATATAAACTATATGG
1 TATATAATTCATTAGTATATATAAACTATATAG
** * * *
1173323 TATAT-ATAAATTA-TATATTATATAGT-TCATTAT
1 TATATAATTCATTAGTATA-TATAAACTAT-A-TAG
** * * * *
1173356 TATAT-ATAAATTA-TATA-GTACA-TATAAAT
1 TATATAATTCATTAGTATATATAAACTATATAG
* *
1173385 TATATAGTTCATTAGTTTATATAAACTATATAG
1 TATATAATTCATTAGTATATATAAACTATATAG
* *
1173418 TATATAGTTCATTAGTATATATAAATTATATAG
1 TATATAATTCATTAGTATATATAAACTATATAG
1173451 TATA
1 TATA
1173455 CACTAAAAAT
Statistics
Matches: 105, Mismatches: 19, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
29 7 0.07
30 7 0.07
31 12 0.11
32 16 0.15
33 63 0.60
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (33 bp):
TATATAATTCATTAGTATATATAAACTATATAG
Found at i:1173353 original size:51 final size:51
Alignment explanation
Indices: 1173290--1173390 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
1173280 ACTAATAAAC
* *
1173290 TATATAATTCATTAGTATATATAAACTATATGGTATATATAAATTATATAT
1 TATATAATTCATTAGTATATATAAACTATATAGTACATATAAATTATATAT
* * *
1173341 TATATAGTTCATTATTATATATAAATTATATAGTACATATAAATTATATA
1 TATATAATTCATTAGTATATATAAACTATATAGTACATATAAATTATATA
1173391 GTTCATTAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (51 bp):
TATATAATTCATTAGTATATATAAACTATATAGTACATATAAATTATATAT
Found at i:1173371 original size:44 final size:44
Alignment explanation
Indices: 1173323--1173419 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
1173313 AACTATATGG
* *
1173323 TATATA-TAAATTATATATTATATAGTTCATTA-TTATATATAAAT
1 TATATAGTAAA-TATAAATTATATAGTTCATTAGTT-TATATAAAC
*
1173367 TATATAGTACATATAAATTATATAGTTCATTAGTTTATATAAAC
1 TATATAGTAAATATAAATTATATAGTTCATTAGTTTATATAAAC
1173411 TATATAGTA
1 TATATAGTA
1173420 TATAGTTCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
44 43 0.90
45 5 0.10
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (44 bp):
TATATAGTAAATATAAATTATATAGTTCATTAGTTTATATAAAC
Found at i:1173382 original size:18 final size:18
Alignment explanation
Indices: 1173290--1173454 Score: 105
Period size: 18 Copynumber: 9.1 Consensus size: 18
1173280 ACTAATAAAC
1173290 TATAT-AATTCAT-TAGTA
1 TATATAAATT-ATATAGTA
* *
1173307 TATATAAACTATATGGTA
1 TATATAAATTATATAGTA
1173325 TATATAAATTATATA-T-
1 TATATAAATTATATAGTA
* *
1173341 TATAT-AGTTCAT-TATTA
1 TATATAAATT-ATATAGTA
1173358 TATATAAATTATATAGTA
1 TATATAAATTATATAGTA
*
1173376 CATATAAATTATATAGT-
1 TATATAAATTATATAGTA
** *
1173393 TCAT-TAGTTTATATAAACTA
1 T-ATATAAATTATAT--AGTA
1173413 TATAGTATATAGTTCAT-TAGTA
1 TATA-TA-A-A-TT-ATATAGTA
1173435 TATATAAATTATATAGTA
1 TATATAAATTATATAGTA
1173453 TA
1 TA
1173455 CACTAAAAAT
Statistics
Matches: 115, Mismatches: 15, Indels: 35
0.70 0.09 0.21
Matches are distributed among these distances:
15 5 0.04
16 8 0.07
17 25 0.22
18 54 0.47
19 5 0.04
20 2 0.02
21 4 0.03
22 7 0.06
24 3 0.03
25 2 0.02
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (18 bp):
TATATAAATTATATAGTA
Found at i:1173578 original size:15 final size:15
Alignment explanation
Indices: 1173517--1173699 Score: 66
Period size: 15 Copynumber: 12.3 Consensus size: 15
1173507 AATCCACCAC
*
1173517 TACATATATTATACA
1 TACATACATTATACA
1173532 CTA-ATTA-ATTATACA
1 -TACA-TACATTATACA
* **
1173547 TAAATACACACATACA
1 TACATACA-TTATACA
1173563 TACATACATTATACA
1 TACATACATTATACA
*
1173578 TTA-ATAAATTATAC-
1 -TACATACATTATACA
*
1173592 -AC--ACATTATACT
1 TACATACATTATACA
*
1173604 TATATATCAATTCATACA
1 TACATA-C-ATT-ATACA
* *
1173622 -ATATACATTATATA
1 TACATACATTATACA
* *
1173636 TTA-TTA-ATTATGCA
1 -TACATACATTATACA
*
1173650 TACATACATTATGCA
1 TACATACATTATACA
* *
1173665 TACGTACATTATGCA
1 TACATACATTATACA
1173680 TTA-ATA-AGTTATACA
1 -TACATACA-TTATACA
1173695 TACAT
1 TACAT
1173700 TATACACGTG
Statistics
Matches: 130, Mismatches: 17, Indels: 41
0.69 0.09 0.22
Matches are distributed among these distances:
11 8 0.06
12 1 0.01
13 3 0.02
14 19 0.15
15 64 0.49
16 23 0.18
17 8 0.06
18 4 0.03
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (15 bp):
TACATACATTATACA
Found at i:1179361 original size:2 final size:2
Alignment explanation
Indices: 1179354--1179396 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1179344 AATCAAACAT
1179354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1179395 TA
1 TA
1179397 AAAATTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1180411 original size:22 final size:22
Alignment explanation
Indices: 1180368--1180412 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1180358 GTCACTACAC
**
1180368 TGATACTAAAGTGCATTTGCAT
1 TGATACTAAAGTGCATCAGCAT
*
1180390 TGATACTAAAGTGCCTCAGCAT
1 TGATACTAAAGTGCATCAGCAT
1180412 T
1 T
1180413 AATAAGAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (22 bp):
TGATACTAAAGTGCATCAGCAT
Found at i:1180741 original size:19 final size:20
Alignment explanation
Indices: 1180705--1180742 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1180695 ATTGAAACTA
1180705 ACCCTTGAGTACCGATACCC
1 ACCCTTGAGTACCGATACCC
*
1180725 ACCCTTG-GTATCGATACC
1 ACCCTTGAGTACCGATACC
1180743 AAAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.24
Consensus pattern (20 bp):
ACCCTTGAGTACCGATACCC
Found at i:1180800 original size:21 final size:21
Alignment explanation
Indices: 1180771--1180829 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
1180761 TTGAGAGAAA
*
1180771 TAGGTAGTATCGATACTTTAGC
1 TAGG-AGTATCGATACTCTAGC
1180793 TAGGAGTATCGATACTCTAGC
1 TAGGAGTATCGATACTCTAGC
*
1180814 TA-AAGTATCGATACTC
1 TAGGAGTATCGATACTC
1180830 CTCTACTGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.37
21 18 0.51
22 4 0.11
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (21 bp):
TAGGAGTATCGATACTCTAGC
Found at i:1180860 original size:34 final size:34
Alignment explanation
Indices: 1180817--1180881 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
1180807 CTCTAGCTAA
1180817 AGTATCGATACTCCTCTACTGGGGTATTGATTAG
1 AGTATCGATACTCCTCTACTGGGGTATTGATTAG
1180851 AGTATCGATACTCCTCTACTGGGGTATTGAT
1 AGTATCGATACTCCTCTACTGGGGTATTGAT
1180882 ACTACCTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (34 bp):
AGTATCGATACTCCTCTACTGGGGTATTGATTAG
Found at i:1187578 original size:3 final size:3
Alignment explanation
Indices: 1187570--1187596 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1187560 ATATAATCTT
1187570 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1187597 ATTTGATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1189013 original size:2 final size:2
Alignment explanation
Indices: 1189006--1189055 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1188996 CAGGTGGAGA
1189006 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
1189048 AT AT AT AT
1 AT AT AT AT
1189056 TGTGGAGCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1194741 original size:90 final size:90
Alignment explanation
Indices: 1194578--1194845 Score: 410
Period size: 90 Copynumber: 3.0 Consensus size: 90
1194568 CATTGTCGTG
* **
1194578 GTTAATTGACGAAATTGAAGAGTATGTTTACATGAATTCAGCAGGACTATTGCAGGTCAATTGGC
1 GTTAA-TGACGAAATTGGAGAGTATGTTCCCATGAATTCAGCAGGACTATTGCAGGTCAATTGGC
* *
1194643 TAGTGCTTTTTTGATAATCATGTAAT
65 TTGTGCTTTTTTGATGATCATGTAAT
* * * * *
1194669 GTTAATGAAGAAATTGGAGAGTACGTTCCCATGAATTCTGCAGGACTATTGCACGTCAGTTGGCT
1 GTTAATGACGAAATTGGAGAGTATGTTCCCATGAATTCAGCAGGACTATTGCAGGTCAATTGGCT
1194734 TGTGCTTTTTTGATGATCATGTAAT
66 TGTGCTTTTTTGATGATCATGTAAT
*
1194759 GTTGATGACGAAATTGGAGAGTATGTTCCCATGAATTCAGCAGGACTATTGCAGGTCAATTGGCT
1 GTTAATGACGAAATTGGAGAGTATGTTCCCATGAATTCAGCAGGACTATTGCAGGTCAATTGGCT
* *
1194824 TGTGCCTCTTTGATGATCATGT
66 TGTGCTTTTTTGATGATCATGT
1194846 GACGTTGGGT
Statistics
Matches: 159, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 154 0.97
91 5 0.03
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (90 bp):
GTTAATGACGAAATTGGAGAGTATGTTCCCATGAATTCAGCAGGACTATTGCAGGTCAATTGGCT
TGTGCTTTTTTGATGATCATGTAAT
Found at i:1201122 original size:182 final size:182
Alignment explanation
Indices: 1200815--1201179 Score: 730
Period size: 182 Copynumber: 2.0 Consensus size: 182
1200805 AATTAAAAGG
1200815 AAACTGAATATGAGTAATTTTAAAATTTCACGGCATCCTTAAGATGTTGGGCCAATATCAACTTC
1 AAACTGAATATGAGTAATTTTAAAATTTCACGGCATCCTTAAGATGTTGGGCCAATATCAACTTC
1200880 ATGCAAGAGAAGTGCAGTTTTATCACGCAATGGTGGAACTCCTTGGTATGCCTTCAGGCGCTAGC
66 ATGCAAGAGAAGTGCAGTTTTATCACGCAATGGTGGAACTCCTTGGTATGCCTTCAGGCGCTAGC
1200945 CATTGACTTTAAAGATAGACCCATCGTCCATGTTCTTGATATCCACAGCGCC
131 CATTGACTTTAAAGATAGACCCATCGTCCATGTTCTTGATATCCACAGCGCC
1200997 AAACTGAATATGAGTAATTTTAAAATTTCACGGCATCCTTAAGATGTTGGGCCAATATCAACTTC
1 AAACTGAATATGAGTAATTTTAAAATTTCACGGCATCCTTAAGATGTTGGGCCAATATCAACTTC
1201062 ATGCAAGAGAAGTGCAGTTTTATCACGCAATGGTGGAACTCCTTGGTATGCCTTCAGGCGCTAGC
66 ATGCAAGAGAAGTGCAGTTTTATCACGCAATGGTGGAACTCCTTGGTATGCCTTCAGGCGCTAGC
1201127 CATTGACTTTAAAGATAGACCCATCGTCCATGTTCTTGATATCCACAGCGCC
131 CATTGACTTTAAAGATAGACCCATCGTCCATGTTCTTGATATCCACAGCGCC
1201179 A
1 A
1201180 TACGGGTAAA
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 183 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (182 bp):
AAACTGAATATGAGTAATTTTAAAATTTCACGGCATCCTTAAGATGTTGGGCCAATATCAACTTC
ATGCAAGAGAAGTGCAGTTTTATCACGCAATGGTGGAACTCCTTGGTATGCCTTCAGGCGCTAGC
CATTGACTTTAAAGATAGACCCATCGTCCATGTTCTTGATATCCACAGCGCC
Done.