Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009608.1 Hibiscus syriacus cultivar Beakdansim tig00116994_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: 1053610
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:840311 original size:20 final size:20
Alignment explanation
Indices: 840260--840311 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
840250 TTTGAAACTT
*
840260 AAATTCGCAACACGAAAATGA
1 AAATT-GCAACGCGAAAATGA
*
840281 AAATCGCAACGCGAAAATGA
1 AAATTGCAACGCGAAAATGA
840301 AAATTGCAACG
1 AAATTGCAACG
840312 TTGCGATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.13
Consensus pattern (20 bp):
AAATTGCAACGCGAAAATGA
Found at i:842099 original size:21 final size:22
Alignment explanation
Indices: 842075--842187 Score: 67
Period size: 21 Copynumber: 5.4 Consensus size: 22
842065 TGGTGCATGG
842075 CGTGATGAGGTATGGT-CTTTA
1 CGTGATGAGGTATGGTACTTTA
* *
842096 CGTGGTGAGGTAGAGGT--TTTA
1 CGTGATGAGGTA-TGGTACTTTA
** ** *
842117 CACGATGA-CAATGGTGCTTTA
1 CGTGATGAGGTATGGTACTTTA
* *
842138 CGTGGTGAGGTAT-CTACTTTA
1 CGTGATGAGGTATGGTACTTTA
* * *
842159 CATGGTGAGGTAT-CTACTTTA
1 CGTGATGAGGTATGGTACTTTA
842180 CGTGATGA
1 CGTGATGA
842188 AGTAGCCGCT
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
19 3 0.04
20 1 0.01
21 61 0.87
22 5 0.07
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (22 bp):
CGTGATGAGGTATGGTACTTTA
Found at i:842519 original size:21 final size:21
Alignment explanation
Indices: 842493--842605 Score: 122
Period size: 21 Copynumber: 5.4 Consensus size: 21
842483 CCTGTCATCA
*
842493 TTCAAGAGGCCTCTCCTATCG
1 TTCAAGAGGCCCCTCCTATCG
* *
842514 TTCAAGAGGCCCCT-ATCATCC
1 TTCAAGAGGCCCCTCCT-ATCG
* *
842535 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCTATCG
*
842556 TTCAAGAGGCCCCT-GTCATCG
1 TTCAAGAGGCCCCTCCT-ATCG
* *
842577 TTCAAGAGGTCCCTCCTACCG
1 TTCAAGAGGCCCCTCCTATCG
842598 TTCAAGAG
1 TTCAAGAG
842606 ACCGATTCAC
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.01
21 73 0.97
22 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCTATCG
Found at i:842533 original size:42 final size:41
Alignment explanation
Indices: 842487--842605 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 41
842477 GATTCACCTG
*
842487 TCATCATTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTA
1 TCATCATTCAAGAGGCC-CTCCTACCGTTCAAGAGGCCCCTA
* * *
842529 TCATCCTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGG-CCCTCCTACCGTTCAAGAGGCCCCTA
*
842571 TCATCGTTCAAGAGGTCCCTCCTACCGTTCAAGAG
1 TCATCATTCAAGAGG-CCCTCCTACCGTTCAAGAG
842606 ACCGATTCAC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 67 0.97
43 2 0.03
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (41 bp):
TCATCATTCAAGAGGCCCTCCTACCGTTCAAGAGGCCCCTA
Found at i:843952 original size:13 final size:13
Alignment explanation
Indices: 843912--843956 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
843902 TTTTTTTTGC
843912 TTGTTTAATTGAT
1 TTGTTTAATTGAT
**
843925 TTGTAAAAGTTGAT
1 TTGTTTAA-TTGAT
843939 TTGTTTAATTGAT
1 TTGTTTAATTGAT
843952 TTGTT
1 TTGTT
843957 GTTTAATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (13 bp):
TTGTTTAATTGAT
Found at i:844049 original size:14 final size:14
Alignment explanation
Indices: 844030--844059 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
844020 GAAAGTCAAA
*
844030 TTCGCGTTGCGATT
1 TTCGCGATGCGATT
844044 TTCGCGATGCGATT
1 TTCGCGATGCGATT
844058 TT
1 TT
844060 GACTTTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.20, G:0.27, T:0.43
Consensus pattern (14 bp):
TTCGCGATGCGATT
Found at i:844111 original size:20 final size:20
Alignment explanation
Indices: 844043--844127 Score: 91
Period size: 20 Copynumber: 4.3 Consensus size: 20
844033 GCGTTGCGAT
* *
844043 TTTCGCGATGCGATTTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * * *
844063 TTTTGCTTTACGAATTTAAC
1 TTTCGCGTTGCGAATTTGAC
*
844083 TTT-GCGTTGCGATTTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
844102 TTTCGCGTTGCGAATTTGTC
1 TTTCGCGTTGCGAATTTGAC
844122 TTTCGC
1 TTTCGC
844128 AACAATCGCA
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.29
20 37 0.71
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:844343 original size:20 final size:20
Alignment explanation
Indices: 844319--844505 Score: 176
Period size: 20 Copynumber: 9.3 Consensus size: 20
844309 ACTCGAAAAT
*
844319 GTTGCGATTTTGACTTTCGT
1 GTTGCGATTTTGACTTTCGC
* *
844339 GTTGCGATTTTTACTTTCGT
1 GTTGCGATTTTGACTTTCGC
*
844359 GTTGCGATTTTTACTTTCGC
1 GTTGCGATTTTGACTTTCGC
* * *
844379 GTTGCGAATTTGATTTTCGT
1 GTTGCGATTTTGACTTTCGC
* * *
844399 GTTGCGAATTTGATTTTTGC
1 GTTGCGATTTTGACTTTCGC
*
844419 GTTGCGGTTTTGACTTTCGC
1 GTTGCGATTTTGACTTTCGC
* * *
844439 GTTGCAAATTTGACTTTTGC
1 GTTGCGATTTTGACTTTCGC
* * * *
844459 GTTGCGAATTTAATTTTTGC
1 GTTGCGATTTTGACTTTCGC
* * * *
844479 CTTGCGGTTTTGAATTTCGT
1 GTTGCGATTTTGACTTTCGC
844499 GTTGCGA
1 GTTGCGA
844506 AAGTGTACCA
Statistics
Matches: 139, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 139 1.00
ACGTcount: A:0.13, C:0.14, G:0.24, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTGACTTTCGC
Found at i:844423 original size:60 final size:60
Alignment explanation
Indices: 844319--844506 Score: 225
Period size: 60 Copynumber: 3.1 Consensus size: 60
844309 ACTCGAAAAT
* * * * * * * * *
844319 GTTGCGATTTTGACTTTCGTGTTGCGATTTTTACTTTCGTGTTGCGATTTTTACTTTCGC
1 GTTGCGAATTTGATTTTCGTGTTGCGAATTTAATTTTTGCGTTGCGGTTTTGACTTTCGC
*
844379 GTTGCGAATTTGATTTTCGTGTTGCGAATTTGATTTTTGCGTTGCGGTTTTGACTTTCGC
1 GTTGCGAATTTGATTTTCGTGTTGCGAATTTAATTTTTGCGTTGCGGTTTTGACTTTCGC
* * * * *
844439 GTTGCAAATTTGACTTTT-GCGTTGCGAATTTAATTTTTGCCTTGCGGTTTTGAATTTCGT
1 GTTGCGAATTTGA-TTTTCGTGTTGCGAATTTAATTTTTGCGTTGCGGTTTTGACTTTCGC
844499 GTTGCGAA
1 GTTGCGAA
844507 AGTGTACCAT
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 107 0.96
61 4 0.04
ACGTcount: A:0.13, C:0.14, G:0.24, T:0.48
Consensus pattern (60 bp):
GTTGCGAATTTGATTTTCGTGTTGCGAATTTAATTTTTGCGTTGCGGTTTTGACTTTCGC
Found at i:847151 original size:24 final size:24
Alignment explanation
Indices: 847117--847170 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
847107 CTGATGCATC
847117 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
847141 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
847165 ATCAAA
1 ATCAAA
847171 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:847184 original size:24 final size:24
Alignment explanation
Indices: 847117--847184 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
847107 CTGATGCATC
* * *
847117 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAGTCTGAATACTGACCAAG
** *
847141 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAGTCTGAATACTGACCAAG
* *
847165 ATCAAATTTTGAATACTGAC
1 ATCAAAGTCTGAATACTGAC
847185 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (24 bp):
ATCAAAGTCTGAATACTGACCAAG
Found at i:848135 original size:20 final size:20
Alignment explanation
Indices: 848110--848282 Score: 63
Period size: 20 Copynumber: 8.7 Consensus size: 20
848100 AAATAAAAGC
848110 TGTTGCGAATTTAAAATTCG
1 TGTTGCGAATTTAAAATTCG
**
848130 TGTTGCGAATCCGAAAA-TCG
1 TGTTGCGAAT-TTAAAATTCG
* * * * *
848150 AGTTGTGAAATCAAAATTCA
1 TGTTGCGAATTTAAAATTCG
*** *
848170 TGTTGCGAAAAGGAAACTT-G
1 TGTTGCG-AATTTAAAATTCG
* **
848190 TGTGATG-AAAAATAAA-TTCG
1 TGT--TGCGAATTTAAAATTCG
* *
848210 CGTTGCGAATTTGAAATTCCG
1 TGTTGCGAATTTAAAATT-CG
* *
848231 TGTTGCGAATTT-GACTTCTG
1 TGTTGCGAATTTAAAATTC-G
848251 TGTTGCG-ATTTACAAATTCG
1 TGTTGCGAATTTA-AAATTCG
*
848271 CGTTGCG-ATTTA
1 TGTTGCGAATTTA
848283 CATATTCGCG
Statistics
Matches: 113, Mismatches: 28, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
18 2 0.02
19 16 0.14
20 64 0.57
21 29 0.26
22 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (20 bp):
TGTTGCGAATTTAAAATTCG
Found at i:848237 original size:21 final size:21
Alignment explanation
Indices: 848203--848258 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
848193 GATGAAAAAT
*
848203 AAATT-CGCGTTGCGAATTTG
1 AAATTCCGTGTTGCGAATTTG
848223 AAATTCCGTGTTGCGAATTTG
1 AAATTCCGTGTTGCGAATTTG
* *
848244 -ACTTCTGTGTTGCGA
1 AAATTCCGTGTTGCGA
848259 TTTACAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (21 bp):
AAATTCCGTGTTGCGAATTTG
Found at i:848283 original size:20 final size:20
Alignment explanation
Indices: 848252--848342 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
848242 TGACTTCTGT
848252 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
848272 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
* * **
848292 GTTACGATTTACATATTATC
1 GTTGCGATTTACAAATTCGC
848312 GTTGCGAATTTGGA-AAATT-GC
1 GTTGCG-ATTT--ACAAATTCGC
848333 GTTGCGATTT
1 GTTGCGATTT
848343 TGGAACCTGT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
20 45 0.74
21 11 0.18
22 4 0.07
23 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:848356 original size:20 final size:20
Alignment explanation
Indices: 848333--848399 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
848323 GGAAAATTGC
848333 GTTGCGATTTTGGAACCTGT
1 GTTGCGATTTTGGAACCTGT
** * ** *
848353 GTTGCGAAATTAG-AGTTCGC
1 GTTGCGATTTTGGAACCT-GT
848373 GTTGCGATTTTGGAACCTGT
1 GTTGCGATTTTGGAACCTGT
848393 GTTGCGA
1 GTTGCGA
848400 AATTGGAGTT
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTTGGAACCTGT
Found at i:848383 original size:40 final size:40
Alignment explanation
Indices: 848331--848424 Score: 170
Period size: 40 Copynumber: 2.4 Consensus size: 40
848321 TTGGAAAATT
848331 GCGTTGCGATTTTGGAACCTGTGTTGCGAAATTAGAGTTC
1 GCGTTGCGATTTTGGAACCTGTGTTGCGAAATTAGAGTTC
*
848371 GCGTTGCGATTTTGGAACCTGTGTTGCGAAATTGGAGTTC
1 GCGTTGCGATTTTGGAACCTGTGTTGCGAAATTAGAGTTC
*
848411 GCGTTGCGAATTTG
1 GCGTTGCGATTTTG
848425 TTGGTCATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.18, C:0.15, G:0.32, T:0.35
Consensus pattern (40 bp):
GCGTTGCGATTTTGGAACCTGTGTTGCGAAATTAGAGTTC
Found at i:848405 original size:20 final size:20
Alignment explanation
Indices: 848342--848406 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
848332 CGTTGCGATT
848342 TTGGAACCTGTGTTGCGAAA
1 TTGGAACCTGTGTTGCGAAA
* ** * **
848362 TTAG-AGTTCGCGTTGCGATT
1 TTGGAACCT-GTGTTGCGAAA
848382 TTGGAACCTGTGTTGCGAAA
1 TTGGAACCTGTGTTGCGAAA
848402 TTGGA
1 TTGGA
848407 GTTCGCGTTG
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.34
Consensus pattern (20 bp):
TTGGAACCTGTGTTGCGAAA
Found at i:848416 original size:20 final size:20
Alignment explanation
Indices: 848353--848420 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
848343 TGGAACCTGT
*
848353 GTTGCGAAATTAGAGTTCGC
1 GTTGCGAAATTGGAGTTCGC
** ** *
848373 GTTGCGATTTTGGA-ACCTGT
1 GTTGCGAAATTGGAGTTC-GC
848393 GTTGCGAAATTGGAGTTCGC
1 GTTGCGAAATTGGAGTTCGC
848413 GTTGCGAA
1 GTTGCGAA
848421 TTTGTTGGTC
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.21, C:0.15, G:0.32, T:0.32
Consensus pattern (20 bp):
GTTGCGAAATTGGAGTTCGC
Found at i:864937 original size:23 final size:23
Alignment explanation
Indices: 864906--864974 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
864896 CACCATAGCT
* *
864906 CGTATAATTGCCCCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
864929 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
864952 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
864975 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:865163 original size:103 final size:103
Alignment explanation
Indices: 864990--865305 Score: 578
Period size: 103 Copynumber: 3.1 Consensus size: 103
864980 TAATGTCCAT
* * * *
864990 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
865055 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
865093 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
865158 TACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
865196 AAGGACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
865261 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
865299 AAGGACC
1 AAGGACC
865306 GCGTAGACCC
Statistics
Matches: 206, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 206 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:870031 original size:2 final size:2
Alignment explanation
Indices: 870024--870050 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
870014 GACATCACTG
870024 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
870051 TAATTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:870814 original size:34 final size:34
Alignment explanation
Indices: 870776--870879 Score: 208
Period size: 34 Copynumber: 3.1 Consensus size: 34
870766 TAATTTTAAA
870776 ATTATGTAGATTGAGTATACCATTCACAACATGG
1 ATTATGTAGATTGAGTATACCATTCACAACATGG
870810 ATTATGTAGATTGAGTATACCATTCACAACATGG
1 ATTATGTAGATTGAGTATACCATTCACAACATGG
870844 ATTATGTAGATTGAGTATACCATTCACAACATGG
1 ATTATGTAGATTGAGTATACCATTCACAACATGG
870878 AT
1 AT
870880 ACGTAATTAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 70 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (34 bp):
ATTATGTAGATTGAGTATACCATTCACAACATGG
Found at i:870940 original size:14 final size:14
Alignment explanation
Indices: 870923--870956 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
870913 TGATTATTAT
*
870923 TAAAATATTAATTG
1 TAAAAAATTAATTG
870937 TAAAAAATTAATTG
1 TAAAAAATTAATTG
870951 TAAAAA
1 TAAAAA
870957 TATACGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (14 bp):
TAAAAAATTAATTG
Found at i:871095 original size:13 final size:14
Alignment explanation
Indices: 871072--871105 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
871062 TTATGTTATT
871072 AAAATATTAATTGC
1 AAAATATTAATTGC
*
871086 AAAA-ATTAATTGT
1 AAAATATTAATTGC
871099 AAAATAT
1 AAAATAT
871106 GTTGTAGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (14 bp):
AAAATATTAATTGC
Found at i:871827 original size:28 final size:26
Alignment explanation
Indices: 871791--871856 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 26
871781 TTTTATATCA
871791 ATTATAGGGTTCAATTTTTTAATACTT
1 ATTATAGGGTTCAATTTTTTAATA-TT
871818 ATTATTAGGGGTTCAATATTTCTTAATATAT
1 ATTA-TA-GGGTTCAAT-TTT-TTAATAT-T
871849 ATTATAGG
1 ATTATAGG
871857 CTTAGTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
27 4 0.12
28 2 0.06
29 11 0.32
30 6 0.18
31 11 0.32
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (26 bp):
ATTATAGGGTTCAATTTTTTAATATT
Found at i:875317 original size:25 final size:27
Alignment explanation
Indices: 875289--875344 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
875279 ATATAAACAT
* *
875289 TAATT-AATATATA-TAATAATATTAA
1 TAATTAAATATAAAGTAATAAAATTAA
875314 TAATTAAAATATAAAGTAATAAAATTAA
1 TAATT-AAATATAAAGTAATAAAATTAA
875342 TAA
1 TAA
875345 CCCAATTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.19
27 7 0.27
28 14 0.54
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
TAATTAAATATAAAGTAATAAAATTAA
Found at i:876598 original size:14 final size:16
Alignment explanation
Indices: 876569--876600 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
876559 GCCTTCAGGC
876569 TTTACAAATAATAATA
1 TTTACAAATAATAATA
876585 TTTA-AAAT-ATAATA
1 TTTACAAATAATAATA
876599 TT
1 TT
876601 ATTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTACAAATAATAATA
Found at i:876616 original size:18 final size:16
Alignment explanation
Indices: 876576--876631 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
876566 GGCTTTACAA
* *
876576 ATAATAATATTTAAAAT
1 ATAATAATATAT-ATAT
*
876593 ATAATATTAT-TATAT
1 ATAATAATATATATAT
876608 ATAATAATATATATAT
1 ATAATAATATATATAT
876624 ATAATAAT
1 ATAATAAT
876632 CATCATCACT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
15 12 0.34
16 14 0.40
17 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATAATATATATAT
Found at i:884429 original size:31 final size:31
Alignment explanation
Indices: 884391--884474 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
884381 AATGTTGAAT
*
884391 AAAAGAAAGAAAAAAAAAATAGCAGTTCGAA
1 AAAAGAAAGAAAAAAAAAAAAGCAGTTCGAA
*
884422 AAAAGAAA-AAAAGAAAAAAAAGCTGTTCGAA
1 AAAAGAAAGAAAA-AAAAAAAAGCAGTTCGAA
* *
884453 AGAA-AAAGAGAGAAAAAAAAAG
1 AAAAGAAAGA-AAAAAAAAAAAG
884475 ACATGAAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 7 0.15
31 37 0.80
32 2 0.04
ACGTcount: A:0.70, C:0.05, G:0.18, T:0.07
Consensus pattern (31 bp):
AAAAGAAAGAAAAAAAAAAAAGCAGTTCGAA
Found at i:886106 original size:18 final size:18
Alignment explanation
Indices: 886060--886102 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
886050 TCTTCTTATT
*
886060 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
886079 TTTATTTAATCACTTTTA
1 TTTATTTAATCACTTTTA
886097 -TTATTT
1 TTTATTT
886103 TAATATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:892325 original size:45 final size:47
Alignment explanation
Indices: 892259--892346 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 47
892249 CAAATCACAT
* * * * *
892259 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTTGGAAAAATAA
1 CCTAACCACATGATTTATAGTTCACATGCATTTATTTAGAAAAATAA
892304 CCTAACCACATGATTTATAGTTCACATGCATTTATTTAGAAAA
1 CCTAACCACATGATTTATAGTTCACATGCATTTATTTAGAAAA
892347 TAAAATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 20 0.56
46 5 0.14
47 11 0.31
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (47 bp):
CCTAACCACATGATTTATAGTTCACATGCATTTATTTAGAAAAATAA
Found at i:894553 original size:32 final size:32
Alignment explanation
Indices: 894466--894567 Score: 113
Period size: 32 Copynumber: 3.2 Consensus size: 32
894456 AGAGTCGAGG
* *
894466 GTTACCTATGTCTTTCA-AGACATATGGACAGT
1 GTTACCTATGTCCTT-AGGGACATATGGACAGT
*
894498 GTTACCTATGTCCTTCGGGACATATGGACAG-
1 GTTACCTATGTCCTTAGGGACATATGGACAGT
*
894529 GATTACCTATGTTC-TAGGGAACATATGGACAGT
1 G-TTACCTATGTCCTTAGGG-ACATATGGACAGT
894562 -TTACCT
1 GTTACCT
894568 TGGTTCTTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
31 11 0.18
32 50 0.82
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (32 bp):
GTTACCTATGTCCTTAGGGACATATGGACAGT
Found at i:894587 original size:31 final size:31
Alignment explanation
Indices: 894484--894593 Score: 116
Period size: 32 Copynumber: 3.5 Consensus size: 31
894474 TGTCTTTCAA
* *
894484 GACATATGGACAGTGTTACCTATGTCCTTCGG
1 GACATATGGACAGT-TTACCTATGTTCTTAGG
*
894516 GACATATGGACAGGATTACCTATGTTC-TAGG
1 GACATATGGACA-GTTTACCTATGTTCTTAGG
*
894547 GAACATATGGACAGTTTACCT-TGGTTCTTTGG
1 G-ACATATGGACAGTTTACCTAT-GTTCTTAGG
* *
894579 GACCTATGGATAGTT
1 GACATATGGACAGTT
894594 GCCGAGGTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
30 1 0.01
31 27 0.40
32 38 0.57
33 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (31 bp):
GACATATGGACAGTTTACCTATGTTCTTAGG
Found at i:895909 original size:19 final size:19
Alignment explanation
Indices: 895864--895901 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
895854 AATCAGATGA
*
895864 AACACCAAATTGTAGAGTC
1 AACACCAAATTATAGAGTC
895883 AACACCAAATTATAGAGTC
1 AACACCAAATTATAGAGTC
895902 GCCACCAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (19 bp):
AACACCAAATTATAGAGTC
Found at i:896300 original size:56 final size:55
Alignment explanation
Indices: 896198--896305 Score: 125
Period size: 56 Copynumber: 1.9 Consensus size: 55
896188 ATATTATAAT
896198 ATTATTATAATTACAAATTATGTAAAATAATAATATAAAAATATAAACATTAATTA
1 ATTATTATAATTACAAATTATGTAAAATAATAATATAAAAATATAAA-ATTAATTA
* *
896254 ATTA-TATAATCTACTAATTAT-TAATAATTAA-AATAT-AAAGTAATAAAATTAA
1 ATTATTATAAT-TACAAATTATGTAA-AA-TAATAATATAAAAAT-ATAAAATTAA
896306 ATAACCTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
55 18 0.39
56 25 0.54
57 3 0.07
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (55 bp):
ATTATTATAATTACAAATTATGTAAAATAATAATATAAAAATATAAAATTAATTA
Found at i:896432 original size:2 final size:2
Alignment explanation
Indices: 896425--896450 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
896415 ATAATTAATC
896425 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
896451 ATGTCTAAAA
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):
TA
Found at i:897548 original size:14 final size:16
Alignment explanation
Indices: 897519--897550 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
897509 GCCTTCGGGC
897519 TTTACAAATAATAATA
1 TTTACAAATAATAATA
897535 TTTA-AAAT-ATAATA
1 TTTACAAATAATAATA
897549 TT
1 TT
897551 ATTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTACAAATAATAATA
Found at i:898281 original size:33 final size:33
Alignment explanation
Indices: 898239--898332 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
898229 ATCCAAGTAG
898239 AAAGATATTAAACCAGTTTTACAAATTATAGGA
1 AAAGATATTAAACCAGTTTTACAAATTATAGGA
* *
898272 AAAGATATTAAACCAGTTTTACAAATTCTAGGC
1 AAAGATATTAAACCAGTTTTACAAATTATAGGA
* *
898305 AAAGATATTAAACCAGTTCTATAAATTA
1 AAAGATATTAAACCAGTTTTACAAATTA
898333 GCTTAATTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.31
Consensus pattern (33 bp):
AAAGATATTAAACCAGTTTTACAAATTATAGGA
Found at i:900113 original size:13 final size:13
Alignment explanation
Indices: 900092--900122 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
900082 GCAAAGACAT
*
900092 TAAACCAGTTTTA
1 TAAATCAGTTTTA
900105 TAAATCAGTTTTA
1 TAAATCAGTTTTA
900118 TAAAT
1 TAAAT
900123 TAGCTTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (13 bp):
TAAATCAGTTTTA
Found at i:901355 original size:13 final size:13
Alignment explanation
Indices: 901337--901364 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
901327 CCTCCATTGA
901337 TTCTAACATCAAT
1 TTCTAACATCAAT
901350 TTCTAACATCAAT
1 TTCTAACATCAAT
901363 TT
1 TT
901365 TCAGCATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (13 bp):
TTCTAACATCAAT
Found at i:902950 original size:16 final size:16
Alignment explanation
Indices: 902927--902963 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
902917 GAAAAAAATG
*
902927 AGAAAATTTGA-AGAA
1 AGAAAAATTGAGAGAA
902942 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
902958 AGAAAA
1 AGAAAA
902964 GAGGAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:903203 original size:2 final size:2
Alignment explanation
Indices: 903196--903237 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
903186 TCATTAAATA
903196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
903237 A
1 A
903238 ATAGATTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:908119 original size:31 final size:31
Alignment explanation
Indices: 908083--908186 Score: 154
Period size: 31 Copynumber: 3.4 Consensus size: 31
908073 CTTTGGGATT
*
908083 TTTCTTGGGTAGGCCCCGTGGCCATGAGATC
1 TTTCTTGGGTAGGCCCCGTGGCCCTGAGATC
* ***
908114 ATTCTTGGGTAGGCCCTACGGCCCTGAGATC
1 TTTCTTGGGTAGGCCCCGTGGCCCTGAGATC
*
908145 TTTCTTGGGTAGGCCCCGTGGCCCTGAGAAC
1 TTTCTTGGGTAGGCCCCGTGGCCCTGAGATC
908176 TTTCTTGGGTA
1 TTTCTTGGGTA
908187 TGCTCTCAGG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.13, C:0.26, G:0.31, T:0.30
Consensus pattern (31 bp):
TTTCTTGGGTAGGCCCCGTGGCCCTGAGATC
Found at i:908120 original size:62 final size:62
Alignment explanation
Indices: 908046--908182 Score: 184
Period size: 62 Copynumber: 2.2 Consensus size: 62
908036 CTGCGGCCCC
* ** * *
908046 GAGATCATTCTTGCGTAGGCCCTTCGACTTTGGGATTTTTCTTGGGTAGGCCCCGTGGCCAT
1 GAGATCATTCTTGCGTAGGCCCTACGACCCTGAGATCTTTCTTGGGTAGGCCCCGTGGCCAT
* * *
908108 GAGATCATTCTTGGGTAGGCCCTACGGCCCTGAGATCTTTCTTGGGTAGGCCCCGTGGCCCT
1 GAGATCATTCTTGCGTAGGCCCTACGACCCTGAGATCTTTCTTGGGTAGGCCCCGTGGCCAT
* *
908170 GAGAACTTTCTTG
1 GAGATCATTCTTG
908183 GGTATGCTCT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.14, C:0.26, G:0.29, T:0.31
Consensus pattern (62 bp):
GAGATCATTCTTGCGTAGGCCCTACGACCCTGAGATCTTTCTTGGGTAGGCCCCGTGGCCAT
Found at i:910054 original size:13 final size:13
Alignment explanation
Indices: 910033--910063 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
910023 GCAAAGACAT
*
910033 TAAACCAGTTTTA
1 TAAATCAGTTTTA
910046 TAAATCAGTTTTA
1 TAAATCAGTTTTA
910059 TAAAT
1 TAAAT
910064 TAGCTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (13 bp):
TAAATCAGTTTTA
Found at i:912972 original size:2 final size:2
Alignment explanation
Indices: 912965--912995 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
912955 TAAATATAAC
912965 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
912996 TTTAAGTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:919292 original size:31 final size:31
Alignment explanation
Indices: 919254--919322 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
919244 GATTTTTTTT
*
919254 GGTAGGCCCCGTGG-CTCTGAGATCTTTCTTG
1 GGTAGGCCCCGTGGCCT-TGAGAACTTTCTTG
919285 GGTAGGCCCCGTGGCCTTGAGAACTTTCTTG
1 GGTAGGCCCCGTGGCCTTGAGAACTTTCTTG
919316 GGTAGGC
1 GGTAGGC
919323 TCTCAGGCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.12, C:0.25, G:0.35, T:0.29
Consensus pattern (31 bp):
GGTAGGCCCCGTGGCCTTGAGAACTTTCTTG
Found at i:922227 original size:19 final size:20
Alignment explanation
Indices: 922203--922248 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
922193 CAAAGTGACC
* *
922203 CAATTTC-ACATTCTAACTT
1 CAATTTCAACACTCTAACAT
922222 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
922242 CAATTTC
1 CAATTTC
922249 TAGCATAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.37
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:925502 original size:12 final size:12
Alignment explanation
Indices: 925485--925509 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
925475 GTTAAATAAT
925485 TTAGGCACCAAA
1 TTAGGCACCAAA
925497 TTAGGCACCAAA
1 TTAGGCACCAAA
925509 T
1 T
925510 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:930135 original size:12 final size:12
Alignment explanation
Indices: 930118--930142 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
930108 GTCAAATAAT
930118 TTAGGCACCAAA
1 TTAGGCACCAAA
930130 TTAGGCACCAAA
1 TTAGGCACCAAA
930142 T
1 T
930143 GGTGATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:932683 original size:20 final size:20
Alignment explanation
Indices: 932640--932687 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
932630 CAAAGTGACC
*
932640 CAATTTC-ACATTCAAACAT
1 CAATTTCAACACTCAAACAT
*
932659 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCAAACAT
*
932679 TAATTTCAA
1 CAATTTCAA
932688 GCATAGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (20 bp):
CAATTTCAACACTCAAACAT
Found at i:934498 original size:371 final size:371
Alignment explanation
Indices: 933806--934555 Score: 1421
Period size: 371 Copynumber: 2.0 Consensus size: 371
933796 AATTGAAAAT
*
933806 TTAATTAAATACATTGAAAGAAGACCTAATAGAATAGTTTAGGATAATTATTGAGTTGAATTAAA
1 TTAATTAAATACATTGAAAGAAGACCTAATAGAATAGTTTAGGACAATTATTGAGTTGAATTAAA
933871 ACTTGGATGAATTGAATTAAACCAATTTACCTAGGAATTGATTTGAATTAAAAGTTAATTAAGAA
66 ACTTGGATGAATTGAATTAAACCAATTTACCTAGGAATTGATTTGAATTAAAAGTTAATTAAGAA
933936 ATTTAGAAAATTGATTTGATCAAATTAAAGTAACCTAATTTCAATTAAATAAAAACATTAGAATT
131 ATTTAGAAAATTGATTTGATCAAATTAAAGTAACCTAATTTCAATTAAATAAAAACATTAGAATT
934001 GAATATAATGAAGAACCTAATTGAGAGGAGTGAAAGAGTAATGACCAAATTACGGTGATCAAGTA
196 GAATATAATGAAGAACCTAATTGAGAGGAGTGAAAGAGTAATGACCAAATTACGGTGATCAAGTA
* *
934066 GGAATTACATACAAATGTTATAATTGCATGCTAAATTTCTAGATTCCTACAATTGCCCTTGAATA
261 GGAATTACATACAAATGTTATAATTGCATGCTAAATTTCTAGATTCCTAAAATTACCCTTGAATA
934131 GTTGATATCTTAAGCATTAAAGCAGGCTAATTAGGACATTTCCATC
326 GTTGATATCTTAAGCATTAAAGCAGGCTAATTAGGACATTTCCATC
934177 TTAATTAAATACATTGAAAGAAGACCTAATAGAATAGTTTAGGACAATTATTGAGTTGAATTAAA
1 TTAATTAAATACATTGAAAGAAGACCTAATAGAATAGTTTAGGACAATTATTGAGTTGAATTAAA
934242 ACTTGGATGAATTGAATTAAACCAATTTACCTAGGAATCT-ATTTGAATTAAAAGTTAATTAAGA
66 ACTTGGATGAATTGAATTAAACCAATTTACCTAGGAAT-TGATTTGAATTAAAAGTTAATTAAGA
*
934306 AATTTAGAAAATTTATTTGATCAAATTAAAGTAACCTAATTTCAATTAAATAAAAACATTAGAAT
130 AATTTAGAAAATTGATTTGATCAAATTAAAGTAACCTAATTTCAATTAAATAAAAACATTAGAAT
934371 TGAATATAATGAAGAACCTAATTGAGAGGAGTGAAAGAGTAATGACCAAATTACGGTGATCAAGT
195 TGAATATAATGAAGAACCTAATTGAGAGGAGTGAAAGAGTAATGACCAAATTACGGTGATCAAGT
*
934436 AGGAATTATATACAAATGTTATAATTGCATGCTAAATTTCTAGATTCCTAAAATTACCCTTGAAT
260 AGGAATTACATACAAATGTTATAATTGCATGCTAAATTTCTAGATTCCTAAAATTACCCTTGAAT
* *
934501 GGTTGATATCTTAAGCATTAAAGGAGGCTAATTAGGACATTTCCATC
325 AGTTGATATCTTAAGCATTAAAGCAGGCTAATTAGGACATTTCCATC
934548 TTAATTAA
1 TTAATTAA
934556 GGATGAAGTG
Statistics
Matches: 371, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
371 370 1.00
372 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (371 bp):
TTAATTAAATACATTGAAAGAAGACCTAATAGAATAGTTTAGGACAATTATTGAGTTGAATTAAA
ACTTGGATGAATTGAATTAAACCAATTTACCTAGGAATTGATTTGAATTAAAAGTTAATTAAGAA
ATTTAGAAAATTGATTTGATCAAATTAAAGTAACCTAATTTCAATTAAATAAAAACATTAGAATT
GAATATAATGAAGAACCTAATTGAGAGGAGTGAAAGAGTAATGACCAAATTACGGTGATCAAGTA
GGAATTACATACAAATGTTATAATTGCATGCTAAATTTCTAGATTCCTAAAATTACCCTTGAATA
GTTGATATCTTAAGCATTAAAGCAGGCTAATTAGGACATTTCCATC
Found at i:934637 original size:15 final size:16
Alignment explanation
Indices: 934617--934653 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
934607 GAAAAAAATG
*
934617 AGAAAAATT-GGAGAA
1 AGAAAAATTAAGAGAA
934632 AGAAAAATTAAGAGAA
1 AGAAAAATTAAGAGAA
934648 AGAAAA
1 AGAAAA
934654 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.68, C:0.00, G:0.22, T:0.11
Consensus pattern (16 bp):
AGAAAAATTAAGAGAA
Found at i:934906 original size:2 final size:2
Alignment explanation
Indices: 934899--934924 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
934889 TATAACATAC
934899 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
934925 GATTCATAAA
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:935410 original size:26 final size:26
Alignment explanation
Indices: 935381--935431 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
935371 TAAAATTATA
*
935381 ATTTAGTCACTAATTTTAATACTTTC
1 ATTTAATCACTAATTTTAATACTTTC
* * *
935407 ATTTAATTACTAGTTTTATTACTTT
1 ATTTAATCACTAATTTTAATACTTT
935432 TTATATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.55
Consensus pattern (26 bp):
ATTTAATCACTAATTTTAATACTTTC
Found at i:935516 original size:40 final size:41
Alignment explanation
Indices: 935437--935516 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 41
935427 ACTTTTTATA
* *
935437 TTTTAATATTATAGTTTTAATTTCATTTATTTTAGTTATTG
1 TTTTAATATTATAGTCTTAATTTCATATATTTTAGTTATTG
*
935478 TTTTAAT-TTATA-TCTTATTTTCAATATATTATTA-TTATT
1 TTTTAATATTATAGTCTTAATTTC-ATATATT-TTAGTTATT
935517 ATTTATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
39 8 0.24
40 16 0.47
41 10 0.29
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (41 bp):
TTTTAATATTATAGTCTTAATTTCATATATTTTAGTTATTG
Found at i:937882 original size:22 final size:21
Alignment explanation
Indices: 937785--937892 Score: 53
Period size: 22 Copynumber: 4.8 Consensus size: 21
937775 ATTACTAGTT
937785 TTATTACTTTTT-ATATTTTAA
1 TTATTA-TTTTTAATATTTTAA
* *
937806 -TATTATAGTTTTAATTTCATTTATT
1 TTATTAT--TTTTAATAT--TTTA-A
937831 TTAGTTATTGTTTAA-ATTTT-A
1 TTA-TTATT-TTTAATATTTTAA
937852 TATACTTATTTTTAATATATTTAA
1 T-TA-TTATTTTTAATAT-TTTAA
* *
937876 TTATTATTATTATTATT
1 TTATTATTTTTAATATT
937893 ATTATTTAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 26
0.67 0.07 0.26
Matches are distributed among these distances:
19 1 0.01
20 5 0.07
21 11 0.16
22 23 0.34
23 8 0.12
24 6 0.09
25 2 0.03
26 7 0.10
27 4 0.06
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (21 bp):
TTATTATTTTTAATATTTTAA
Found at i:937886 original size:47 final size:44
Alignment explanation
Indices: 937783--937886 Score: 104
Period size: 47 Copynumber: 2.2 Consensus size: 44
937773 TAATTACTAG
* *
937783 TTTTATTACTTTTTATATTTTAATATTATAGTTTTAATTTCATTTA
1 TTTTATTA-TTTTTAAATTTTAATATTATA-TTTTAATATCATTTA
937829 TTTTAGTTATTGTTTAAATTTTATATACTTAT-TTTTAATAT-ATTTAA
1 TTTTA-TTATT-TTTAAATTTTA-ATA-TTATATTTTAATATCATTT-A
937876 TTATTATTATT
1 TT-TTATTATT
937887 ATTATTATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
46 11 0.22
47 29 0.58
48 6 0.12
49 4 0.08
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (44 bp):
TTTTATTATTTTTAAATTTTAATATTATATTTTAATATCATTTA
Found at i:941985 original size:36 final size:36
Alignment explanation
Indices: 941938--942006 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
941928 CTATGCACAG
* *
941938 AAAGATCCTATTATATTAATACCAAAAGTATTCCAC
1 AAAGATCCTATTAGATTAATACCAAAAGCATTCCAC
*
941974 AAAGATCCTATTAGATTGATACCAAAAGCATTC
1 AAAGATCCTATTAGATTAATACCAAAAGCATTC
942007 TATGGAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (36 bp):
AAAGATCCTATTAGATTAATACCAAAAGCATTCCAC
Found at i:942732 original size:6 final size:6
Alignment explanation
Indices: 942721--942773 Score: 70
Period size: 6 Copynumber: 8.5 Consensus size: 6
942711 TATTCACATC
* *
942721 TTTGCA TTTGCA TTTGCA TTTTCA TTTGCA TTTTCA TTTGCA TCTTTGCA
1 TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA --TTTGCA
942771 TTT
1 TTT
942774 TTATATTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 35 0.85
8 6 0.15
ACGTcount: A:0.15, C:0.17, G:0.11, T:0.57
Consensus pattern (6 bp):
TTTGCA
Found at i:946050 original size:7 final size:7
Alignment explanation
Indices: 946040--946086 Score: 85
Period size: 7 Copynumber: 6.6 Consensus size: 7
946030 AAAAAAGGGG
946040 AAAAGGA
1 AAAAGGA
946047 AAAAGGA
1 AAAAGGA
946054 AAAAGGA
1 AAAAGGA
946061 AAAAGGA
1 AAAAGGA
946068 AAAAGGAA
1 AAAAGG-A
946076 AAAAGGA
1 AAAAGGA
946083 AAAA
1 AAAA
946087 ATTAAATCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 32 0.82
8 7 0.18
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAAAGGA
Found at i:946064 original size:21 final size:22
Alignment explanation
Indices: 946030--946086 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
946020 ATAAAAAATA
*
946030 AAAAAAGGGGAAAAGGAAAAAGG
1 AAAAAA-GGAAAAAGGAAAAAGG
946053 -AAAAAGGAAAAAGGAAAAAGG
1 AAAAAAGGAAAAAGGAAAAAGG
946074 AAAAAAGGAAAAA
1 AAAAAAGGAAAAA
946087 ATTAAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAAAAGGAAAAAGGAAAAAGG
Found at i:949423 original size:75 final size:74
Alignment explanation
Indices: 949333--949476 Score: 198
Period size: 75 Copynumber: 1.9 Consensus size: 74
949323 ACAAGAAGAA
* * * *
949333 AATGTGGAGCATGCTGAAAGCCCATTTCAATCATAATCAGGAATAATGACATATTTTGAACGTTT
1 AATGTGGAGCATGCTGAAAGCCCATTTCAATAAGAATCAGGAATAATGACACATTTTGAACGCTT
949398 GTATTAGCC
66 GTATTAGCC
* * ** *
949407 AATGTTGGGGCATGCTGAAAGCCCCTTTCAATAAGAATCAGGAATGTTGACGCATTTTGAACGCT
1 AATG-TGGAGCATGCTGAAAGCCCATTTCAATAAGAATCAGGAATAATGACACATTTTGAACGCT
949472 TGTAT
65 TGTAT
949477 CAGCAAATCT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 4 0.07
75 56 0.93
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (74 bp):
AATGTGGAGCATGCTGAAAGCCCATTTCAATAAGAATCAGGAATAATGACACATTTTGAACGCTT
GTATTAGCC
Found at i:950600 original size:24 final size:24
Alignment explanation
Indices: 950573--950702 Score: 140
Period size: 24 Copynumber: 5.5 Consensus size: 24
950563 ATATATCAAA
* * *
950573 ATCAAATCATAATTCATGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
* * *
950597 ATCATATCAAAATCCAGGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
*
950621 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
* *
950645 ATC--ATAAGAATCCATGT-TAGAT
1 ATCAGATCAGAATCCATGTCAAG-T
*
950667 ATCAGATCATAATCCATGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
950691 ATCAGATCAGAA
1 ATCAGATCAGAA
950703 ATCAAATCGA
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
21 2 0.02
22 16 0.18
24 68 0.77
25 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (24 bp):
ATCAGATCAGAATCCATGTCAAGT
Found at i:954918 original size:21 final size:21
Alignment explanation
Indices: 954849--954924 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 21
954839 ATCTACATTC
*
954849 TTCAAAGATGATAGA-TACACT
1 TTCAAAGATGATAGATTA-TCT
*
954870 CTTCAAAGATGATAGATTCTCTT
1 -TTCAAAGATGATAGATTATC-T
954893 TTCAAAGATGATAGATTATCT
1 TTCAAAGATGATAGATTATCT
954914 TTCAAAGATGA
1 TTCAAAGATGA
954925 AAGCCTTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.24
22 35 0.71
23 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (21 bp):
TTCAAAGATGATAGATTATCT
Found at i:955670 original size:36 final size:34
Alignment explanation
Indices: 955625--955746 Score: 93
Period size: 36 Copynumber: 3.4 Consensus size: 34
955615 TAGTAATTTA
955625 TCTCACTTGAGATTATTTTTCTTAAAACAAACTGTG
1 TCTCACTTGAGATTATTTTTCTTAAAACAAA-T-TG
* * ** * *
955661 TCTCGCTTGAGA-CAGTTTCACTTGAAACTACAATTTA
1 TCTCACTTGAGATTA-TTTTTCTT-AAA--ACAAATTG
*
955698 TCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCG
1 TCTCACTTGAGATTATTTTTCTTAAAACAA-ATT-G
*
955734 TCTCGCTTGAGAT
1 TCTCACTTGAGAT
955747 AGTTTCATTA
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
34 4 0.06
35 3 0.05
36 32 0.49
37 21 0.32
38 1 0.02
39 4 0.06
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (34 bp):
TCTCACTTGAGATTATTTTTCTTAAAACAAATTG
Found at i:955738 original size:73 final size:73
Alignment explanation
Indices: 955619--955761 Score: 220
Period size: 73 Copynumber: 2.0 Consensus size: 73
955609 TTCAAATAGT
955619 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCACTT
1 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCA-TT
955684 -GAAACTAC
65 AGAAACTAC
* *
955692 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGA-T-TCGTCTCGCTTGAGATAGTTTCAT
1 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAA-ACTGT-GTCTCGCTTGAGACAGTTTCAT
955755 TAGAAAC
64 TAGAAAC
955762 AAAAATTTCC
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
72 3 0.05
73 61 0.94
74 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCATTA
GAAACTAC
Found at i:955762 original size:36 final size:35
Alignment explanation
Indices: 955660--955764 Score: 90
Period size: 36 Copynumber: 2.9 Consensus size: 35
955650 AACAAACTGT
* *
955660 GTCTCGCTTGAGACAGTTTCACTT-GAAACTACAATTT
1 GTCTCGCTTGAGATAGTTTCA-TTAGAAAC-A-AATTC
* * *
955697 ATCTCACTTGAGATTGTTTTTC-TTA-AAACAAGATTC
1 GTCTCGCTTGAGATAG--TTTCATTAGAAACAA-ATTC
955733 GTCTCGCTTGAGATAGTTTCATTAGAAACAAA
1 GTCTCGCTTGAGATAGTTTCATTAGAAACAAA
955765 AATTTCCATC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
34 4 0.07
35 5 0.09
36 23 0.43
37 18 0.33
39 4 0.07
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (35 bp):
GTCTCGCTTGAGATAGTTTCATTAGAAACAAATTC
Found at i:955777 original size:73 final size:73
Alignment explanation
Indices: 955619--955777 Score: 200
Period size: 73 Copynumber: 2.2 Consensus size: 73
955609 TTCAAATAGT
*
955619 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCACTT
1 AATTTACCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCACTT
* *
955684 GAAACTAC
66 GAAACAAA
* * *
955692 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGA-T-TCGTCTCGCTTGAGATAGTTTCA-
1 AATTTACCTCACTTGAGATTATTTTTCTTAAAACAA-ACTGT-GTCTCGCTTGAGACAGTTTCAC
955754 TTAGAAACAAA
64 TT-GAAACAAA
955765 AATTT-CCATCACT
1 AATTTACC-TCACT
955778 CGATGGATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
72 4 0.05
73 72 0.94
74 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (73 bp):
AATTTACCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCACTT
GAAACAAA
Found at i:956193 original size:224 final size:225
Alignment explanation
Indices: 955777--956226 Score: 640
Period size: 224 Copynumber: 2.0 Consensus size: 225
955767 TTTCCATCAC
* *
955777 TCGATGGATCAACATTTCTAGAGGAAGTTCATAATGAGAAGAAGTCATTTGAAGAGGAAGAAGAA
1 TCGATGGATCAACATTTCTAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAA
* * * * *
955842 GTTCATAATAGGAACAACTTGTTCAACCTTTTGCTCGATTCTATCTCGGAAGGAGATAAATCAGC
66 GTTCATAATAGGAACAACTTGTTCAACCTTTTGCTCGACTCCATCTCAGAAAGAGATAAAGCAGC
955907 ACCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGGAGTTCATA
131 ACCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGGAGTTCATA
* *
955972 ATGAGAAGAACTTGTTCAACTTTAGCTTGA
196 ATGAGAAGAACTTGTTCAACCTTAACTTGA
* *
956002 TCGATGGATCAA-ATTTTTCAGA-GAA-TTCATAATGAGGAGAACTCATCTGAAGAGGAAGAAGA
1 TCGATGGATCAACATTTCT-AGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGA
* * * * *
956064 AGTTCATAAT-GAGAAGAACTTGTTCAACCTTTTGCTTGACTCCATTTCTATAAAGAGATAGAGC
65 AGTTCATAATAG-GAACAACTTGTTCAACCTTTTGCTCGACTCCATCTC-AGAAAGAGATAAAGC
* * *
956128 AGCA-GAGCCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGGAGTT
128 AGCACCA-ACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGGAGTT
* *
956192 CATAATGAGAAGAATTTGTTCGACCTTAACTTGA
192 CATAATGAGAAGAACTTGTTCAACCTTAACTTGA
956226 T
1 T
956227 TCATCACCTA
Statistics
Matches: 200, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
222 1 0.00
223 76 0.38
224 108 0.54
225 15 0.08
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (225 bp):
TCGATGGATCAACATTTCTAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAA
GTTCATAATAGGAACAACTTGTTCAACCTTTTGCTCGACTCCATCTCAGAAAGAGATAAAGCAGC
ACCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGGAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAACTTGA
Found at i:956457 original size:139 final size:140
Alignment explanation
Indices: 956136--956488 Score: 393
Period size: 139 Copynumber: 2.6 Consensus size: 140
956126 GCAGCAGAGC
* * *
956136 CATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATGA
1 CATTTCCAGAG-AGAGTTCATAATGAAAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGA
* * * * *
956200 GAAGAATTTGTTC-GACCTTAACTTGATTCATCACCTATGGAGTTGAATGAAAGAAGAACCTCAC
65 GAAGAACTTGTTCAAACCTTAACTTAATTCATCACCTATGAAGTTGAATCAAAGAAGAACCTCAC
*
956264 TTGAGGATCAA
130 TTAAGGATCAA
** *
956275 CATTTTTAGAGAAAGTTCATAAT-AAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGA
1 CATTTCCAGAGAGAGTTCATAATGAA-AAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGA
** * * * *
956339 GAAGAACTTGTTCAAACCTTGCCTTAATTCATCACTTATGAAGTTGAATCAATG-A-CACCTC-T
65 GAAGAACTTGTTCAAACCTTAACTTAATTCATCACCTATGAAGTTGAATCAAAGAAGAACCTCAC
*
956401 TTCAAGGATCAG
130 TT-AAGGATCAA
* * *
956413 CATTTCCAGA-AGGAGTTCATAATGAAAAGAAATCATATG-AAA--AAGAAGAAGTTCATAACGA
1 CATTTCCAGAGA-GAGTTCATAATGAAAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGA
*
956474 GAAGAACTTATTCAA
65 GAAGAACTTGTTCAA
956489 CTTTTTTCTA
Statistics
Matches: 182, Mismatches: 26, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
135 32 0.18
137 6 0.03
138 42 0.23
139 69 0.38
140 33 0.18
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (140 bp):
CATTTCCAGAGAGAGTTCATAATGAAAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAAACCTTAACTTAATTCATCACCTATGAAGTTGAATCAAAGAAGAACCTCACT
TAAGGATCAA
Found at i:956714 original size:3 final size:3
Alignment explanation
Indices: 956706--956784 Score: 101
Period size: 3 Copynumber: 26.3 Consensus size: 3
956696 TTTTATTTAT
956706 TTA TTA TTA TTCA -TA TTA TTA TT- TTA TTTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
956750 TTA TTA TTTA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
956785 ATTCCCAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
2 5 0.07
3 56 0.82
4 7 0.10
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:958172 original size:41 final size:41
Alignment explanation
Indices: 958127--958207 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
958117 ACTTTTTATA
958127 TTTTAATATTATA-GTTTTAATTTCAAT-TATTTTACTTATTG
1 TTTTAATATTATATG-TTTAATTTCAATATATTTTA-TTATTG
* *
958168 TTTTAATTTTATATGTTTATTTTCAATATATTTTATTATT
1 TTTTAATATTATATGTTTAATTTCAATATATTTTATTATT
958208 ATTATTTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 28 0.78
42 8 0.22
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (41 bp):
TTTTAATATTATATGTTTAATTTCAATATATTTTATTATTG
Found at i:958209 original size:22 final size:21
Alignment explanation
Indices: 958147--958210 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
958137 ATAGTTTTAA
*
958147 TTTCAATTATTTTACTTATTGT
1 TTTCAATTATTTTA-TTATTAT
*
958169 TTT-AATT-TTATATGT-TTAT
1 TTTCAATTATTTTAT-TATTAT
958188 TTTCAATATATTTTATTATTAT
1 TTTCAAT-TATTTTATTATTAT
958210 T
1 T
958211 ATTTAGTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
19 7 0.21
20 8 0.24
21 6 0.18
22 13 0.38
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTCAATTATTTTATTATTAT
Found at i:958481 original size:2 final size:2
Alignment explanation
Indices: 958439--958470 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
958429 ATTTATAAAA
958439 AT AT -T 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 A
958471 AGTTAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:961061 original size:20 final size:20
Alignment explanation
Indices: 961027--961072 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
961017 AAGTGACCCG
*
961027 ATTTC-ACATTCTAACATCA
1 ATTTCAACACTCTAACATCA
*
961046 ATTTCAACACTCTAACATTA
1 ATTTCAACACTCTAACATCA
961066 ATTTCAA
1 ATTTCAA
961073 GCATAGTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTTCAACACTCTAACATCA
Found at i:962934 original size:8 final size:9
Alignment explanation
Indices: 962896--962935 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
962886 TAATCATTAA
*
962896 ATATAACAT
1 ATATAATAT
962905 ATAT-ATAT
1 ATATAATAT
962913 ATAT-ATAT
1 ATATAATAT
962921 ATATAATAT
1 ATATAATAT
962930 -TATAAT
1 ATATAAT
962936 TGATTCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATAATAT
Found at i:966398 original size:15 final size:14
Alignment explanation
Indices: 966369--966408 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
966359 AATGGGAAGT
966369 AATCCCTGCAAAAA
1 AATCCCTGCAAAAA
*
966383 AATCCCTGCGAAAA
1 AATCCCTGCAAAAA
*
966397 AATCTCTGCAAA
1 AATCCCTGCAAA
966409 TAGACAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.28, G:0.10, T:0.17
Consensus pattern (14 bp):
AATCCCTGCAAAAA
Found at i:967465 original size:20 final size:20
Alignment explanation
Indices: 967429--967476 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
967419 CAAAGTGACC
*
967429 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
*
967448 CAATTTCAACACTCTAACTT
1 CAATTTCAACACTCTAACAT
*
967468 TAATTTCAA
1 CAATTTCAA
967477 GCATAGTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:969002 original size:15 final size:15
Alignment explanation
Indices: 968984--969016 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
968974 AAAAAATGAG
968984 AAAATTG-GAGAAAGA
1 AAAATTGAGAG-AAGA
968999 AAAATTGAGAGAAGA
1 AAAATTGAGAGAAGA
969014 AAA
1 AAA
969017 GAGGATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (15 bp):
AAAATTGAGAGAAGA
Found at i:969260 original size:2 final size:2
Alignment explanation
Indices: 969253--969278 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
969243 ATTAAATAAC
969253 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
969279 TATGATTGAT
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:971209 original size:20 final size:20
Alignment explanation
Indices: 971184--971290 Score: 128
Period size: 20 Copynumber: 5.3 Consensus size: 20
971174 AAATCACAAT
*
971184 GCGATACTGACTATCGCAAC
1 GCGATACTGACTTTCGCAAC
* *
971204 GCGATAAT-ACAAAATT-GCAAC
1 GCGATACTGAC---TTTCGCAAC
971225 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
971245 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
*
971265 GCGATACTAACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
*
971285 GAGATA
1 GCGATA
971291 ATACAGAATC
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
19 4 0.05
20 56 0.75
21 12 0.16
22 3 0.04
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (20 bp):
GCGATACTGACTTTCGCAAC
Found at i:971218 original size:41 final size:41
Alignment explanation
Indices: 971173--971310 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
971163 GCGGATTGGT
* * *
971173 AAAATCACAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
971214 AAAATTGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** * *
971256 --TTTCGCAACGCGATACTAACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
971295 AGAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
971311 TTTCAAAGTT
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 45 0.56
42 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:971463 original size:12 final size:12
Alignment explanation
Indices: 971444--971477 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
971434 CTCTCTGGCG
971444 ACATCCGTTCCT
1 ACATCCGTTCCT
*
971456 ATATCCGTTCCT
1 ACATCCGTTCCT
971468 ACATCC-TTCC
1 ACATCCGTTCC
971478 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:971651 original size:20 final size:20
Alignment explanation
Indices: 971626--971683 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
971616 ATTCATTTGA
971626 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
971646 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
971666 CTATCACAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
971684 CGCAATGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:971733 original size:19 final size:19
Alignment explanation
Indices: 971711--971756 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
971701 GATTTTCTCG
971711 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
971730 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
971749 TTGCGATT
1 TTGCGATT
971757 CTCTCGTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:971915 original size:14 final size:14
Alignment explanation
Indices: 971896--971932 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
971886 CATCAATTAA
971896 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
971910 ACAAATCATCTTTT
1 ACAAATCAACATTT
971924 ACAAATCAA
1 ACAAATCAA
971933 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:972553 original size:75 final size:75
Alignment explanation
Indices: 972462--972611 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
972452 ATCATTTATT
972462 TGCGCACTTATTTATGAACACCTTTAAAAAAATTAAAAAATAAACACTAACCTTATCGACCTCAC
1 TGCGCACTTATTTATGAACACCTTTAAAAAAATTAAAAAATAAACACTAACCTTATCGACCTCAC
972527 ACCATGCAGG
66 ACCATGCAGG
972537 TGCGCACTTATTTATGAACACCTTTAAAAAAATTAAAAAATAAACACTAACCTTATCGACCTCAC
1 TGCGCACTTATTTATGAACACCTTTAAAAAAATTAAAAAATAAACACTAACCTTATCGACCTCAC
972602 ACCATGCAGG
66 ACCATGCAGG
972612 ATAACGTCGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.25
Consensus pattern (75 bp):
TGCGCACTTATTTATGAACACCTTTAAAAAAATTAAAAAATAAACACTAACCTTATCGACCTCAC
ACCATGCAGG
Found at i:973293 original size:20 final size:20
Alignment explanation
Indices: 973268--973315 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
973258 TGAAAATGAA
*
973268 ATCGCAACACGAAA-ATGGCT
1 ATCGCAACAC-AAATATGACT
*
973288 ATCGCAACACAAATTTGACT
1 ATCGCAACACAAATATGACT
973308 ATCGCAAC
1 ATCGCAAC
973316 GAGAGAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.19
Consensus pattern (20 bp):
ATCGCAACACAAATATGACT
Found at i:973645 original size:17 final size:19
Alignment explanation
Indices: 973609--973645 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
973599 GGATTTCGTC
*
973609 GAGATGGATGAGAGAGTGA
1 GAGATGGATGAGAGACTGA
973628 GAGATGGATG-G-GACTGA
1 GAGATGGATGAGAGACTGA
973645 G
1 G
973646 TTGTGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 1 0.06
19 10 0.59
ACGTcount: A:0.32, C:0.03, G:0.49, T:0.16
Consensus pattern (19 bp):
GAGATGGATGAGAGACTGA
Found at i:973860 original size:20 final size:20
Alignment explanation
Indices: 973808--973932 Score: 114
Period size: 20 Copynumber: 6.3 Consensus size: 20
973798 TATTATATCG
* *
973808 TTGCG-AAGTCAGAATCGCG
1 TTGCGAAAGTCAGTATCGCA
*
973827 TTGCGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCA
*
973847 TTGCGAAAGTCAGTATCTC-
1 TTGCGAAAGTCAGTATCGCA
** *
973866 TTGCGATTTTGT-ATTATCGCA
1 TTGCGA--AAGTCAGTATCGCA
* *
973887 TTGCGATAGTAAGTATCGCA
1 TTGCGAAAGTCAGTATCGCA
973907 TTGC-AATAGTCAGTATCGCA
1 TTGCGAA-AGTCAGTATCGCA
973927 TTGCGA
1 TTGCGA
973933 TTTTCCCAAT
Statistics
Matches: 89, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
19 15 0.17
20 65 0.73
21 9 0.10
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
TTGCGAAAGTCAGTATCGCA
Found at i:973885 original size:60 final size:61
Alignment explanation
Indices: 973821--973936 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 61
973811 CGAAGTCAGA
* * * *
973821 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAA-AGTCAGTATCTC-TTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGTATCGCATTGC-AATAGTCAGTATCGCATTGCGATTTTGTATT
*
973881 ATCGCATTGCGATAGTAAGTATCGCATTGCAATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGTATCGCATTGCAATAGTCAGTATCGCATTGCGATTTT
973937 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 2 0.04
60 37 0.76
61 10 0.20
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGTATCGCATTGCAATAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:975973 original size:20 final size:20
Alignment explanation
Indices: 975937--975984 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
975927 CAAAGTGACC
*
975937 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
975956 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
975976 TAATTTCAA
1 CAATTTCAA
975985 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:979193 original size:49 final size:50
Alignment explanation
Indices: 979136--979248 Score: 210
Period size: 50 Copynumber: 2.3 Consensus size: 50
979126 GTTCTGTTGA
*
979136 ACAAAGAACTTGTTATCTGAG-TTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTTATTCTACCAATTCAACAACTCAGAGC
979185 ACAAAGAACTTGTTATCAGAGTTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTTATTCTACCAATTCAACAACTCAGAGC
979235 ACAAAGAACTTGTT
1 ACAAAGAACTTGTT
979249 CTAACCGCTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
49 20 0.32
50 42 0.68
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.28
Consensus pattern (50 bp):
ACAAAGAACTTGTTATCAGAGTTTATTCTACCAATTCAACAACTCAGAGC
Found at i:979450 original size:84 final size:83
Alignment explanation
Indices: 979305--979478 Score: 330
Period size: 84 Copynumber: 2.1 Consensus size: 83
979295 TCGATCTGTG
979305 AAAACTACAAAATGGAGATGAAAGCTGTCATTGGCATTCTTTGCTGGTAATCAGTTTACCGGTAG
1 AAAA-TACAAAATGGAGATGAAAGCTGTCATTGGCATTCTTTGCTGGTAATCAGTTTACCGGTAG
979370 TATCATAGCGTGTATGGTT
65 TATCATAGCGTGTATGGTT
979389 AAAATACAAAATGGAGATTGAAAGCTGTCATTGGCATTCTTTGCTGGTAATCAGTTTACCGGTAG
1 AAAATACAAAATGGAGA-TGAAAGCTGTCATTGGCATTCTTTGCTGGTAATCAGTTTACCGGTAG
979454 TATCATAGCGTGTATGGTT
65 TATCATAGCGTGTATGGTT
979473 AAAATA
1 AAAATA
979479 AACAGATTCA
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
83 13 0.15
84 76 0.85
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (83 bp):
AAAATACAAAATGGAGATGAAAGCTGTCATTGGCATTCTTTGCTGGTAATCAGTTTACCGGTAGT
ATCATAGCGTGTATGGTT
Found at i:981370 original size:20 final size:20
Alignment explanation
Indices: 981334--981381 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
981324 CAAAGTGACC
*
981334 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
981353 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
981373 TAATTTCAA
1 CAATTTCAA
981382 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:984620 original size:49 final size:49
Alignment explanation
Indices: 984563--984674 Score: 224
Period size: 49 Copynumber: 2.3 Consensus size: 49
984553 GTTTTGTTGA
984563 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
984612 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
984661 ACAAAGAACTTGTT
1 ACAAAGAACTTGTT
984675 CTAACCGCTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (49 bp):
ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
Found at i:986718 original size:20 final size:20
Alignment explanation
Indices: 986682--986729 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
986672 CCAAAGTGCC
*
986682 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
986701 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
986721 TAATTTCAA
1 CAATTTCAA
986730 TAGTACATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:986823 original size:24 final size:25
Alignment explanation
Indices: 986795--986843 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
986785 TCAAATAGGC
986795 CCCCAATGTTCAC-AAATTACAAAA
1 CCCCAATGTTCACAAAATTACAAAA
986819 CCCCAATGTTCACAAAATTACAAAA
1 CCCCAATGTTCACAAAATTACAAAA
986844 GAGTCCCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.47, C:0.29, G:0.04, T:0.20
Consensus pattern (25 bp):
CCCCAATGTTCACAAAATTACAAAA
Found at i:990678 original size:146 final size:148
Alignment explanation
Indices: 990492--990784 Score: 547
Period size: 146 Copynumber: 2.0 Consensus size: 148
990482 TGGAAGGATA
990492 ACAAGCTTCATCCTCAAGGGTCCCATATGTCTCACTGAGCCGACCTTAAATGGACCATCATCTTT
1 ACAAGCTTCATCCTCAAGGGTCCCATATGTCTCACTGAGCCGACCTTAAATGGACCATCATCTTT
*
990557 TC-TTTGCTATCTCCTATTCGTTATCCTCACCCGGCTT-AACTATATGGAATAACTGAGCTTGAA
66 TCTTTTGCTATCTCCTATTCGCTATCCTCACCCGGCTTAAACTATATGGAATAACTGAGCTTGAA
990620 TT-CTACTTTATAACCAGG
131 TTCCTAC-TTATAACCAGG
990638 ACAAGCTTCATCCTCAAGGGTCCCATATGTCTCACTGAGCCGACCTTAAATGGACCATCATCTTT
1 ACAAGCTTCATCCTCAAGGGTCCCATATGTCTCACTGAGCCGACCTTAAATGGACCATCATCTTT
990703 TCTTTTGCTATCTCCTATTCGCTATCCTCACCCGGCTTAAACTATATGGAATAACTGAGCTTGAA
66 TCTTTTGCTATCTCCTATTCGCTATCCTCACCCGGCTTAAACTATATGGAATAACTGAGCTTGAA
990768 TTCCTACTTATAACCAG
131 TTCCTACTTATAACCAG
990785 TGTTTCTCTC
Statistics
Matches: 143, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
146 67 0.47
147 34 0.24
148 38 0.27
149 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (148 bp):
ACAAGCTTCATCCTCAAGGGTCCCATATGTCTCACTGAGCCGACCTTAAATGGACCATCATCTTT
TCTTTTGCTATCTCCTATTCGCTATCCTCACCCGGCTTAAACTATATGGAATAACTGAGCTTGAA
TTCCTACTTATAACCAGG
Found at i:992187 original size:20 final size:19
Alignment explanation
Indices: 992150--992196 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
992140 CAAAGTGACC
*
992150 CAATTTC-ACATTTAACAT
1 CAATTTCAACATCTAACAT
992168 CAATTTCAACACTCTAACAT
1 CAATTTCAACA-TCTAACAT
*
992188 TAATTTCAA
1 CAATTTCAA
992197 GCATAGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.28
19 3 0.12
20 15 0.60
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.36
Consensus pattern (19 bp):
CAATTTCAACATCTAACAT
Found at i:993500 original size:16 final size:16
Alignment explanation
Indices: 993477--993513 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
993467 AGAAAAAATG
*
993477 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
993492 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
993508 AGAAAA
1 AGAAAA
993514 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:994257 original size:34 final size:35
Alignment explanation
Indices: 994214--994283 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
994204 AAGACGGGTT
994214 CTAGCGTCAC-AATACGTAACTTTACAAGGACCCG
1 CTAGCGTCACAAATACGTAACTTTACAAGGACCCG
994248 CTAGCGTCACAAATACGTAACTTTACAAGGACCCG
1 CTAGCGTCACAAATACGTAACTTTACAAGGACCCG
994283 C
1 C
994284 ACCCTGATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 10 0.29
35 25 0.71
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (35 bp):
CTAGCGTCACAAATACGTAACTTTACAAGGACCCG
Found at i:997256 original size:20 final size:20
Alignment explanation
Indices: 997220--997267 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
997210 CAAAGTGACC
*
997220 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
997239 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
997259 TAATTTCAA
1 CAATTTCAA
997268 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:998849 original size:16 final size:16
Alignment explanation
Indices: 998826--998862 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
998816 AAAAAAAATG
*
998826 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
998841 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
998857 AGAAAA
1 AGAAAA
998863 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:1001621 original size:10 final size:10
Alignment explanation
Indices: 1001606--1001630 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1001596 TATATATAAA
1001606 AATTATTTTT
1 AATTATTTTT
1001616 AATTATTTTT
1 AATTATTTTT
1001626 AATTA
1 AATTA
1001631 ATAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
AATTATTTTT
Found at i:1002604 original size:20 final size:20
Alignment explanation
Indices: 1002568--1002615 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1002558 CGAAGTGACC
*
1002568 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
1002587 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
1002607 TAATTTCAA
1 CAATTTCAA
1002616 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:1003707 original size:23 final size:24
Alignment explanation
Indices: 1003668--1003712 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1003658 ATTTGAGCTT
1003668 TAAATTAATTGAATTAC-AAAAGA
1 TAAATTAATTGAATTACGAAAAGA
*
1003691 TAAATTAAATTG-CTTACGAAAA
1 TAAATT-AATTGAATTACGAAAA
1003713 TGAATCAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (24 bp):
TAAATTAATTGAATTACGAAAAGA
Found at i:1004196 original size:16 final size:16
Alignment explanation
Indices: 1004173--1004209 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1004163 GAAAAAAATG
*
1004173 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
1004188 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
1004204 AGAAAA
1 AGAAAA
1004210 GAGATTTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:1004455 original size:2 final size:2
Alignment explanation
Indices: 1004448--1004484 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1004438 TAAATATAAC
1004448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1004485 TATGATTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1007976 original size:20 final size:20
Alignment explanation
Indices: 1007940--1007987 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1007930 CAAAGTGACC
*
1007940 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
1007959 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
1007979 TAATTTCAA
1 CAATTTCAA
1007988 GCATAGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:1008023 original size:16 final size:16
Alignment explanation
Indices: 1007997--1008034 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1007987 AGCATAGTAT
1007997 ATATT-AAACAATTAC
1 ATATTGAAACAATTAC
1008012 ATATTGAAACAATTAC
1 ATATTGAAACAATTAC
1008028 ATATTGA
1 ATATTGA
1008035 TCTTTAGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (16 bp):
ATATTGAAACAATTAC
Found at i:1009763 original size:2 final size:2
Alignment explanation
Indices: 1009756--1009797 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1009746 TAAATATAAC
1009756 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
1009798 TATGATTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1013220 original size:20 final size:20
Alignment explanation
Indices: 1013177--1013224 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1013167 CAAAGTGACC
*
1013177 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
*
1013196 CAATTTCAACACTCTAGCAT
1 CAATTTCAACACTCTAACAT
*
1013216 TAATTTCAA
1 CAATTTCAA
1013225 GCATAGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:1018358 original size:23 final size:24
Alignment explanation
Indices: 1018331--1018400 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
1018321 CCTAACCTAA
1018331 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* * * *
1018354 ATTCTAATCTGATACATCACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
1018378 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
1018401 ATTTATGTTT
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 13 0.36
24 23 0.64
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1022308 original size:31 final size:31
Alignment explanation
Indices: 1022273--1022347 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1022263 CTAATGTGAC
*
1022273 TCTTGGGTAGGATCTT-CGACCTCGAGATCAT
1 TCTTGGGTAGG-CCTTGCGACCTCGAGATCAT
* * **
1022304 TCTTGGGTAGGCCTTGCGACCTTGGGATTTT
1 TCTTGGGTAGGCCTTGCGACCTCGAGATCAT
1022335 TCTTGGGTAGGCC
1 TCTTGGGTAGGCC
1022348 CCGTGGCCCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 3 0.08
31 35 0.92
ACGTcount: A:0.13, C:0.21, G:0.31, T:0.35
Consensus pattern (31 bp):
TCTTGGGTAGGCCTTGCGACCTCGAGATCAT
Found at i:1022441 original size:31 final size:30
Alignment explanation
Indices: 1022373--1022442 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 30
1022363 CATTATTGAA
*
1022373 TAGGCCCTGAGATCTTTCTTGGGTAGGCCC
1 TAGGCCCTGAGAACTTTCTTGGGTAGGCCC
*
1022403 TATGGCCCTGAGAACTTTCTTGGGTAGGCTC
1 TA-GGCCCTGAGAACTTTCTTGGGTAGGCCC
1022434 TCAGGCCCT
1 T-AGGCCCT
1022443 AAGATGCTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 2 0.06
31 33 0.92
32 1 0.03
ACGTcount: A:0.14, C:0.27, G:0.29, T:0.30
Consensus pattern (30 bp):
TAGGCCCTGAGAACTTTCTTGGGTAGGCCC
Found at i:1023461 original size:20 final size:20
Alignment explanation
Indices: 1023436--1023475 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1023426 ATAGCGTGTA
*
1023436 TGGTTAAAATATAACAGATT
1 TGGTTAAAATAGAACAGATT
1023456 TGGTTAAAATAGAACAGATT
1 TGGTTAAAATAGAACAGATT
1023476 CAGCTTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (20 bp):
TGGTTAAAATAGAACAGATT
Found at i:1026724 original size:16 final size:16
Alignment explanation
Indices: 1026701--1026737 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1026691 AGAAAAAATG
*
1026701 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
1026716 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
1026732 AGAAAA
1 AGAAAA
1026738 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:1026983 original size:2 final size:2
Alignment explanation
Indices: 1026976--1027020 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1026966 TAAAAATAAC
1026976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1027017 -T AT A
1 AT AT A
1027021 ATTGATTCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.