Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 98 of 208
Found at i:29368399 original size:120 final size:120
Alignment explanation
Indices: 29368254--29368492 Score: 433
Period size: 120 Copynumber: 2.0 Consensus size: 120
29368244 ATTTTGTTTG
*
29368254 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
1 AACCTATTTGTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
* * *
29368319 TTAGACAGCAAGTATGCATTTTGTTTGAACCTATTTTTATATTTAATAAAATATA
66 TTAAACAGAAAGTATGCATTTTGTTTGAACCTATTTGTATATTTAATAAAATATA
*
29368374 AACCTATTTGTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTATAAT
1 AACCTATTTGTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
29368439 TTAAACAGAAAGTATGCATTTTGTTTGAACCTATTTGTATATTTAATAAAATAT
66 TTAAACAGAAAGTATGCATTTTGTTTGAACCTATTTGTATATTTAATAAAATAT
29368493 TTGTATATAT
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 114 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (120 bp):
AACCTATTTGTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
TTAAACAGAAAGTATGCATTTTGTTTGAACCTATTTGTATATTTAATAAAATATA
Found at i:29368402 original size:92 final size:92
Alignment explanation
Indices: 29367978--29368386 Score: 746
Period size: 92 Copynumber: 4.4 Consensus size: 92
29367968 TACAATTTTT
* *
29367978 AACCTATTTGTATATTTAATAAAATATGAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
1 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
29368043 TTAAACAGCAAGTATGCATTTTGTTTG
66 TTAAACAGCAAGTATGCATTTTGTTTG
*
29368070 AACCTATTTGTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
1 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
*
29368135 TTAAACAGCAAGTATGCGTTTTGTTTG
66 TTAAACAGCAAGTATGCATTTTGTTTG
* *
29368162 AACCTATTTTTATATTTAATAAAATATAAACCCATTTGTATCAAAGTATGCACATAAGCTACAAT
1 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
*
29368227 TTAAACAGCAAGTATGAATTTTGTTTG
66 TTAAACAGCAAGTATGCATTTTGTTTG
29368254 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
1 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
*
29368319 TTAGACAGCAAGTATGCATTTTGTTTG
66 TTAAACAGCAAGTATGCATTTTGTTTG
29368346 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTAT
1 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTAT
29368387 ATTTAATAAA
Statistics
Matches: 306, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 306 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (92 bp):
AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
TTAAACAGCAAGTATGCATTTTGTTTG
Found at i:29370653 original size:9 final size:9
Alignment explanation
Indices: 29370639--29370688 Score: 82
Period size: 9 Copynumber: 5.6 Consensus size: 9
29370629 TTGCAAAAAG
29370639 GACGATGAC
1 GACGATGAC
29370648 GACGATGAC
1 GACGATGAC
*
29370657 AACGATGAC
1 GACGATGAC
29370666 GACGATGAC
1 GACGATGAC
*
29370675 GATGATGAC
1 GACGATGAC
29370684 GACGA
1 GACGA
29370689 GGTTTCTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.36, C:0.20, G:0.32, T:0.12
Consensus pattern (9 bp):
GACGATGAC
Found at i:29371777 original size:9 final size:9
Alignment explanation
Indices: 29371761--29371804 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
29371751 TTTTGTTACA
29371761 ACAATTAAT
1 ACAATTAAT
*
29371770 ATAATTAAT
1 ACAATTAAT
29371779 ACAATT-A-
1 ACAATTAAT
29371786 ACAATTAAT
1 ACAATTAAT
29371795 ACAATTAAT
1 ACAATTAAT
29371804 A
1 A
29371805 ATTTGATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 6 0.19
8 2 0.06
9 23 0.74
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (9 bp):
ACAATTAAT
Found at i:29371793 original size:16 final size:16
Alignment explanation
Indices: 29371772--29371807 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
29371762 CAATTAATAT
29371772 AATTAATACAATTAAC
1 AATTAATACAATTAAC
*
29371788 AATTAATACAATTAAT
1 AATTAATACAATTAAC
29371804 AATT
1 AATT
29371808 TGATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTAATACAATTAAC
Found at i:29371898 original size:16 final size:16
Alignment explanation
Indices: 29371877--29371918 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
29371867 AATAATTTGA
*
29371877 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
29371893 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
29371909 TATTTTTAAT
1 TAATTTTAAT
29371919 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:29371902 original size:22 final size:23
Alignment explanation
Indices: 29371892--29371947 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
29371882 TTACTAACAA
* * *
29371892 TTAATTTTAAT-AACAATTATTT
1 TTAATTTTAATAAAAAAATAATT
*
29371914 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
29371937 TTAATTTTAAT
1 TTAATTTTAAT
29371948 GCAAAACGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:29376115 original size:683 final size:683
Alignment explanation
Indices: 29374810--29376177 Score: 2077
Period size: 683 Copynumber: 2.0 Consensus size: 683
29374800 TAACTACTGA
* *
29374810 GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAGAAGGGTATCAGATGGACCATAGCCG
1 GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAGAAGGCTATCAGATGGACCATAGCCA
* * *
29374875 ATATTCGCAGAATTAGTCCATCTATATGCATGCACAAGATTATCTTAGAAAATGACGAAAAGGGT
66 ATATTCACAAAATTAGTCCATCTATATGCATGCACAAGATTATCTTAGAAAATGACGAAAAGAGT
* *
29374940 ACGATTAATGGACAACGAAGACTGAACCCTATCTTGAAGGACGTAGTCAAGAAAGAAATCATCAA
131 ACGATTAATGGACAACGAAGACTGAACCCCATCATGAAGGACGTAGTCAAGAAAGAAATCATCAA
*
29375005 GTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGTCTGATCCAGTGCG
196 GTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGTCAGATCCAGTGCG
* *
29375070 TGCCAAAGAAAAGACGTATCACGGTCATTAAGAAGAAGAATAATGAGTTGATACCGACTAGAACG
261 TGCCAAAGAAAAGACGTATCACGGTCATTAAGAAGAAGAATAACGAGTTGATACCGAATAGAACG
* *
29375135 GTGACGGGATGGAGAATTTGCATCAATTACTAGAAGCTGAACAAGGCAACTAGGAAAGATCACTT
326 GTGACGGGATGGAGAATTTGCATCAATTACGAGAAGCTGAACAAGGCAACTAGAAAAGATCACTT
** *
29375200 TCCTTTGTCGTTTTTGGACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTGTTTTCTCG
391 TCCTTTGTCGTTTTTACACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTATTTTCTCG
* * * * * * * * *
29375265 ATGGATACTTGGGGTATATTCAGATTATAGTAGCATCGAAAGATCAGCACAAGACAACATTCACC
456 ATGGATACTCGGGGTATAATCAAATTACAGTAGCACCGAAAGATAAACAAAAGAAAACATTCACC
* *
29375330 TGCCCGTATGGTACGCTTTCATTTAGGCACATGCCATTTGATTTATGTAATGCACCTGCTACATT
521 TGCCCGTACGGTACGCTTGCATTTAGGCACATGCCATTTGATTTATGTAATGCACCTGCTACATT
* *
29375395 TCAAAGAAGTATGATGTCTATTTTTACTGACATGGTTGAGAAATATTTGGAAGTTTTTATGGATG
586 TCAAAGAAGTATAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTTTATGGATG
29375460 ATTTTTCAGTATTCAGAGATACATATGATGATT
651 ATTTTTCAGTATTCAGAGATACATATGATGATT
* * *
29375493 GCAAGAAGAGAAACTCATCCTGGTGTTGAAACAATTCAAGAAGGCTATCGGATGGACCATAGCTA
1 GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAGAAGGCTATCAGATGGACCATAGCCA
* * *
29375558 ATATTCACAAAATTAGTCCATCTGTATGCATGCACAAGATTATCTTAGAAGATGGCGAAAAAGAG
66 ATATTCACAAAATTAGTCCATCTATATGCATGCACAAGATTATCTTAGAAAATGACG-AAAAGAG
* * *
29375623 -ACGATTGATGGTCAACGAAGACTGAACCCCATCATGAAGGATGTAGTCAAGAAAGAAATCATCA
130 TACGATTAATGGACAACGAAGACTGAACCCCATCATGAAGGACGTAGTCAAGAAAGAAATCATCA
**
29375687 AGTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATGGGTAAGTCCAG-TCCAGTG
195 AGTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGT-CAGATCCAGTG
* * *
29375751 CGTGCTAAAGAAAAGAGGTATCACGGTCATTGAA-AATG-AGAATAACGATTTGATACCGAATAG
259 CGTGCCAAAGAAAAGACGTATCACGGTCATT-AAGAA-GAAGAATAACGAGTTGATACCGAATAG
* * *
29375814 AACGGTTACGGGATGGAGAATTTGCATCGATTATCGA-AAGCTGAACTAGGCAACTAGAAAAGAT
322 AACGGTGACGGGATGGAGAATTTGCATCAATTA-CGAGAAGCTGAACAAGGCAACTAGAAAAGAT
* *
29375878 CACTTTCCTTTG-CTGTTTTTACACCAGATGCTGGATAGACTCGTAGGGCGAGACTATTACTATT
386 CACTTTCCTTTGTC-GTTTTTACACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTATT
*
29375942 TTCTCGATGGGTACTCGGGGTATAATCAAATTACAGTAGCACC-AGAAGATAAACAAAAGAAAAC
450 TTCTCGATGGATACTCGGGGTATAATCAAATTACAGTAGCACCGA-AAGATAAACAAAAGAAAAC
* * * * *
29376006 ATTCACCTTCTCGTACGGTAC-ATCTGCATTTAGGCGCATGCCATTTGGTTTATGTAATGCACCT
514 ATTCACCTGCCCGTACGGTACGCT-TGCATTTAGGCACATGCCATTTGATTTATGTAATGCACCT
* * * *
29376070 GCTACATTTTAAATATGTCTAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTT
578 GCTACATTTCAAAGAAGTATAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTT
* *
29376135 TATGGATGATTTTTTAGTATTCGGAGATACATATGATGATT
643 TATGGATGATTTTTCAGTATTCAGAGATACATATGATGATT
29376176 GC
1 GC
29376178 CTAAACAATC
Statistics
Matches: 618, Mismatches: 59, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
682 3 0.00
683 602 0.97
684 13 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (683 bp):
GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAGAAGGCTATCAGATGGACCATAGCCA
ATATTCACAAAATTAGTCCATCTATATGCATGCACAAGATTATCTTAGAAAATGACGAAAAGAGT
ACGATTAATGGACAACGAAGACTGAACCCCATCATGAAGGACGTAGTCAAGAAAGAAATCATCAA
GTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGTCAGATCCAGTGCG
TGCCAAAGAAAAGACGTATCACGGTCATTAAGAAGAAGAATAACGAGTTGATACCGAATAGAACG
GTGACGGGATGGAGAATTTGCATCAATTACGAGAAGCTGAACAAGGCAACTAGAAAAGATCACTT
TCCTTTGTCGTTTTTACACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTATTTTCTCG
ATGGATACTCGGGGTATAATCAAATTACAGTAGCACCGAAAGATAAACAAAAGAAAACATTCACC
TGCCCGTACGGTACGCTTGCATTTAGGCACATGCCATTTGATTTATGTAATGCACCTGCTACATT
TCAAAGAAGTATAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTTTATGGATG
ATTTTTCAGTATTCAGAGATACATATGATGATT
Found at i:29382214 original size:21 final size:20
Alignment explanation
Indices: 29382169--29382214 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
29382159 TTTTCGGAAT
29382169 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
29382188 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
29382209 GGTTGA
1 GGTTGA
29382215 TTGCATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:29383752 original size:20 final size:19
Alignment explanation
Indices: 29383712--29383754 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
29383702 ATTGAACTTG
*
29383712 AAAATTGGACTAGAGATCA
1 AAAATTGGACTAGAGACCA
29383731 AAAATTGGAACTA-AGAACCA
1 AAAATTGG-ACTAGAG-ACCA
29383751 AAAA
1 AAAA
29383755 CTGAGATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATTGGACTAGAGACCA
Found at i:29383753 original size:19 final size:19
Alignment explanation
Indices: 29383712--29383754 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
29383702 ATTGAACTTG
*
29383712 AAAATTGGACTAGAGATCA
1 AAAATTGGACTAGAGAACA
29383731 AAAATTGGAACTA-AGAACCA
1 AAAATTGG-ACTAGAGAA-CA
29383751 AAAA
1 AAAA
29383755 CTGAGATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATTGGACTAGAGAACA
Found at i:29384224 original size:20 final size:20
Alignment explanation
Indices: 29384129--29384231 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
29384119 TGATAATATT
29384129 TTATTAATTTAATATTAAAG
1 TTATTAATTTAATATTAAAG
* * *
29384149 TGATTAACTTAATATTAAAT
1 TTATTAATTTAATATTAAAG
* *
29384169 TTAATCTAATATTTATATTGATAATCAT
1 TT-AT-TAAT-TTAATA-T--TAA--AG
29384197 TATATTAATTTAATATTAAAG
1 T-TATTAATTTAATATTAAAG
29384218 TTATTAAGTTTAAT
1 TTATTAA-TTTAAT
29384232 CATAGTTGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
20 24 0.37
21 10 0.15
22 3 0.05
23 8 0.12
24 1 0.02
25 1 0.02
26 8 0.12
27 4 0.06
28 5 0.08
29 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TTATTAATTTAATATTAAAG
Found at i:29385140 original size:14 final size:14
Alignment explanation
Indices: 29385123--29385149 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29385113 TATTTTCTAT
29385123 TTCTATTTTTTTTC
1 TTCTATTTTTTTTC
29385137 TTCTATTTTTTTT
1 TTCTATTTTTTTT
29385150 TTGGTTTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCTATTTTTTTTC
Found at i:29385140 original size:20 final size:19
Alignment explanation
Indices: 29385102--29385144 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
29385092 TTTAGTTTGG
*
29385102 ATTTTTATTTTTATTTTCT
1 ATTTCTATTTTTATTTTCT
*
29385121 ATTTCTATTTTTTTTCTTCT
1 ATTTCTATTTTTATT-TTCT
29385141 ATTT
1 ATTT
29385145 TTTTTTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTTCTATTTTTATTTTCT
Found at i:29386511 original size:83 final size:83
Alignment explanation
Indices: 29386365--29386525 Score: 198
Period size: 83 Copynumber: 1.9 Consensus size: 83
29386355 TGATCTGATC
* * * * * * *
29386365 TGGTAGTTTAATAGCAACATATTTGTATAGCGGTTTATCGCAATGCAATGTACTGTATCTACGTC
1 TGGTAGTTTAATAGCAACATATCTATACAGCGGTTTACCACAATGCAATGTACTGCATATACGTC
*
29386430 AAATTTGTTGCGTTTGTT
66 AAATTTGCTGCGTTTGTT
* *
29386448 TGGTAGTTTAACT-GCAACATATCTATACAGTGGTTTACCACAATGCATTGTACTGCATATACGT
1 TGGTAGTTTAA-TAGCAACATATCTATACAGCGGTTTACCACAATGCAATGTACTGCATATACGT
* *
29386512 TAACTTTGCTGCGT
65 CAAATTTGCTGCGT
29386526 ATTATTATCT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
83 64 0.98
84 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (83 bp):
TGGTAGTTTAATAGCAACATATCTATACAGCGGTTTACCACAATGCAATGTACTGCATATACGTC
AAATTTGCTGCGTTTGTT
Found at i:29387697 original size:72 final size:72
Alignment explanation
Indices: 29387608--29387751 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
29387598 TATTCAAAGG
*
29387608 ATTCACAATGACCAGTTAATTTAATTTCATTTTCGAACTTCAATTGTTTACTTAAATAATAATTC
1 ATTCACAATGACCAGTTAATTTAATTTCATTTTCAAACTTCAATTGTTTACTTAAATAATAATTC
29387673 GAAAAAC
66 GAAAAAC
* *
29387680 ATTCACAATGACTAGTTAATTTAATTTCATTTTCAAACTTCAATTTTTTACTTAAATAATAATTC
1 ATTCACAATGACCAGTTAATTTAATTTCATTTTCAAACTTCAATTGTTTACTTAAATAATAATTC
29387745 GAAAAAC
66 GAAAAAC
29387752 TTAACTTAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (72 bp):
ATTCACAATGACCAGTTAATTTAATTTCATTTTCAAACTTCAATTGTTTACTTAAATAATAATTC
GAAAAAC
Found at i:29389977 original size:50 final size:50
Alignment explanation
Indices: 29389883--29390116 Score: 211
Period size: 50 Copynumber: 4.6 Consensus size: 50
29389873 GATCCCATAA
* * *
29389883 AAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCTCATGT
1 AAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCCCATGT
**
29389939 AAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCCCGT
1 AAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGT
* * * **
29389989 AAGACCATGCCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGT
1 AAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGT
* * * * * **
29390039 AAGACCATATCTGGGATATGGCATTGGCA--GTACAAGAAACATCCCATGT
1 AAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTCCCATGT
* * *
29390088 AATACCATGTCTGGGACATGACTTTGGCA
1 AAGACCATGTCTGGGACATGGCATTGGCA
29390117 TGTTATTATC
Statistics
Matches: 151, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.25
50 81 0.54
53 3 0.02
55 1 0.01
56 28 0.19
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
AAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGT
Found at i:29396659 original size:18 final size:18
Alignment explanation
Indices: 29396613--29396663 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
29396603 AGCTCTCAGG
29396613 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* ***
29396631 CAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
29396649 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
29396664 CTTCATTCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.43, G:0.04, T:0.39
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:29399671 original size:32 final size:33
Alignment explanation
Indices: 29399635--29399722 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 33
29399625 AACTTTTCCG
*
29399635 GAAAATATTTT-CAGGAAATC-TGCCAAACAACA
1 GAAAATATTTTACAGCAAATCAT-CCAAACAACA
* *
29399667 GAAAATATTTTACA-CAGATTCATCCAAACACCA
1 GAAAATATTTTACAGCA-AATCATCCAAACAACA
* *
29399700 GAAAATATTTTCCAGTAAATCAT
1 GAAAATATTTTACAGCAAATCAT
29399723 TTTCCAGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
32 12 0.26
33 32 0.70
34 2 0.04
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCATCCAAACAACA
Found at i:29399719 original size:14 final size:15
Alignment explanation
Indices: 29399697--29399773 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
29399687 CATCCAAACA
29399697 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
29399711 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
29399726 CCAGAAAAGTAAATCATATT
1 CCAG---A--AAATCATTTT
29399746 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
29399760 CC-GAAAAACATTTT
1 CCAGAAAATCATTTT
29399774 ACTGTCAAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
13 1 0.02
14 28 0.55
15 9 0.18
20 13 0.25
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:29399738 original size:20 final size:20
Alignment explanation
Indices: 29399713--29399752 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29399703 AATATTTTCC
*
29399713 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATATTCCAGAAA
29399733 AGTAAATCATATTCCAGAAA
1 AGTAAATCATATTCCAGAAA
29399753 TCATTTTCCG
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:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAATCATATTCCAGAAA
Found at i:29403144 original size:11 final size:11
Alignment explanation
Indices: 29403130--29403155 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29403120 TCCGGCCAGG
29403130 GGCCGGTCATC
1 GGCCGGTCATC
29403141 GGCCGGTCATC
1 GGCCGGTCATC
29403152 GGCC
1 GGCC
29403156 ACCACGCCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.38, G:0.38, T:0.15
Consensus pattern (11 bp):
GGCCGGTCATC
Found at i:29414543 original size:28 final size:28
Alignment explanation
Indices: 29414503--29414557 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
29414493 ATAAGTGGGA
29414503 GATCCAACACTTAATGCATGTTATATTT
1 GATCCAACACTTAATGCATGTTATATTT
* **
29414531 GATCCAACGCTTAATGTGTGTTATATT
1 GATCCAACACTTAATGCATGTTATATT
29414558 GCAATAGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (28 bp):
GATCCAACACTTAATGCATGTTATATTT
Found at i:29415457 original size:21 final size:21
Alignment explanation
Indices: 29415419--29415458 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29415409 TAATAATGTC
*
29415419 TCAAAACATTAAGAACATACA
1 TCAAAACATCAAGAACATACA
* *
29415440 TCAAAACCTCAAGTACATA
1 TCAAAACATCAAGAACATA
29415459 ATTAATTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.20
Consensus pattern (21 bp):
TCAAAACATCAAGAACATACA
Found at i:29415537 original size:68 final size:68
Alignment explanation
Indices: 29415447--29415594 Score: 248
Period size: 68 Copynumber: 2.2 Consensus size: 68
29415437 ACATCAAAAC
* *
29415447 CTCAAG-T-ACATAATTAATTATTTGGAGCATATCGCAAATTTTGGTCTTGAGAGTAAACAAACA
1 CTCAAGATAACATGATTAATTATTTGGAGCATATCGCAAATTTTGGTCTTGAGACTAAACAAACA
29415510 AAT
66 AAT
*
29415513 CTCAAGATAACATGATTAATTATTTGGTGCATATCGCAAATTTTGGTCTTGAGACTAAACAAACA
1 CTCAAGATAACATGATTAATTATTTGGAGCATATCGCAAATTTTGGTCTTGAGACTAAACAAACA
29415578 AAT
66 AAT
29415581 CTC-AGATAACATGA
1 CTCAAGATAACATGA
29415595 CTCAAATCTC
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
66 6 0.08
67 12 0.16
68 59 0.77
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (68 bp):
CTCAAGATAACATGATTAATTATTTGGAGCATATCGCAAATTTTGGTCTTGAGACTAAACAAACA
AAT
Found at i:29415803 original size:35 final size:35
Alignment explanation
Indices: 29415757--29415824 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
29415747 CCTAATTGCA
29415757 TTAAATAATATCATTTGAGATTTGTTAAACATGCG
1 TTAAATAATATCATTTGAGATTTGTTAAACATGCG
29415792 TTAAATAATATCATTTGAGATTTGTTAAACATG
1 TTAAATAATATCATTTGAGATTTGTTAAACATG
29415825 TTTATGTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.41
Consensus pattern (35 bp):
TTAAATAATATCATTTGAGATTTGTTAAACATGCG
Found at i:29437304 original size:25 final size:25
Alignment explanation
Indices: 29437223--29437338 Score: 105
Period size: 25 Copynumber: 4.6 Consensus size: 25
29437213 GCGGACACAC
29437223 CACAGCTCGTATGAGCTTACCAAGTT
1 CACAGCTCGTATGAGCTTACCAA-TT
* * *
29437249 -GCAGCACGTGA-GAGCTTACCGATT
1 CACAGCTCGT-ATGAGCTTACCAATT
*
29437273 CCCAGCTCGTATGAGCTTACCAATT
1 CACAGCTCGTATGAGCTTACCAATT
*
29437298 CACAGCTTGCG-A-GAGCATACCAATT
1 CACAGC-T-CGTATGAGCTTACCAATT
* *
29437323 CATAGCTCTTATGAGC
1 CACAGCTCGTATGAGC
29437339 ATACATGTAC
Statistics
Matches: 73, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
23 1 0.01
24 5 0.07
25 62 0.85
26 3 0.04
27 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (25 bp):
CACAGCTCGTATGAGCTTACCAATT
Found at i:29437312 original size:50 final size:50
Alignment explanation
Indices: 29437223--29437338 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
29437213 GCGGACACAC
* * * *
29437223 CACAGCTCGTATGAGCTTACCAAGTTGCAGCACGTGAGAGCTTACCGATT
1 CACAGCTCGTATGAGCTTACCAAGTTACAGCACGCGAGAGCATACCAATT
* **
29437273 CCCAGCTCGTATGAGCTTACCAA-TTCACAGCTTGCGAGAGCATACCAATT
1 CACAGCTCGTATGAGCTTACCAAGTT-ACAGCACGCGAGAGCATACCAATT
* *
29437323 CATAGCTCTTATGAGC
1 CACAGCTCGTATGAGC
29437339 ATACATGTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 2 0.04
50 53 0.96
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (50 bp):
CACAGCTCGTATGAGCTTACCAAGTTACAGCACGCGAGAGCATACCAATT
Found at i:29442977 original size:16 final size:16
Alignment explanation
Indices: 29442956--29442990 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
29442946 TTTGGTTCGC
29442956 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAAG
*
29442972 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAAG
29442988 TGT
1 TGT
29442991 CATAGCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAGAAG
Found at i:29443254 original size:14 final size:15
Alignment explanation
Indices: 29443215--29443256 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29443205 TTTTAACATA
*
29443215 ATTATTATTAAATAT
1 ATTATAATTAAATAT
29443230 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
29443244 A-TATAATTTAATA
1 ATTATAATTAAATA
29443257 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:29443566 original size:24 final size:27
Alignment explanation
Indices: 29443515--29443567 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
29443505 TATATGTAAT
*
29443515 ATTATTAAAATAATATTTTTTATTTTA
1 ATTATTAAAATAATATTTTTTATATTA
*
29443542 ATTATTTAAA-AATA-TTTTTA-ATTA
1 ATTATTAAAATAATATTTTTTATATTA
29443566 AT
1 AT
29443568 GCGGTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 6 0.25
26 4 0.17
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATTAAAATAATATTTTTTATATTA
Found at i:29445929 original size:25 final size:25
Alignment explanation
Indices: 29445874--29445955 Score: 96
Period size: 25 Copynumber: 3.3 Consensus size: 25
29445864 GCGGACACAC
29445874 CACAGCTCGTATGAGCTTACCAAGTT
1 CACAGCTCGTATGAGCTTACCAA-TT
* *
29445900 -GCAGCTCGTGA-GAGCTTACCGATT
1 CACAGCTCGT-ATGAGCTTACCAATT
* *
29445924 CTCAGCTCGTATGAGCTTACAAATT
1 CACAGCTCGTATGAGCTTACCAATT
29445949 CACAGCT
1 CACAGCT
29445956 TGTGAGAGCA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 3 0.06
25 43 0.91
26 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.27
Consensus pattern (25 bp):
CACAGCTCGTATGAGCTTACCAATT
Found at i:29445955 original size:50 final size:50
Alignment explanation
Indices: 29445876--29445994 Score: 143
Period size: 50 Copynumber: 2.4 Consensus size: 50
29445866 GGACACACCA
* * *
29445876 CAGCTCGTATGAGCTTACCAAGTTGCAGCTCGTGAGAGCTTACCGATTC-T
1 CAGCTCGTATGAGCTTA-CAAATTACAGCTCGTGAGAGCATACCGATTCAT
* *
29445926 CAGCTCGTATGAGCTTACAAATTCACAGCTTGTGAGAGCATATCGATTCAT
1 CAGCTCGTATGAGCTTACAAATT-ACAGCTCGTGAGAGCATACCGATTCAT
* *
29445977 -AGCTCTTATGAGCATACA
1 CAGCTCGTATGAGCTTACA
29445995 TGTACATGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
49 5 0.08
50 54 0.90
51 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTACAAATTACAGCTCGTGAGAGCATACCGATTCAT
Found at i:29447773 original size:20 final size:20
Alignment explanation
Indices: 29447750--29447811 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
29447740 ATACTTTCGA
29447750 TTTAATCCATAAACTTACAG
1 TTTAATCCATAAACTTACAG
* * *
29447770 TTT-AT--TTAATACTTTCAA
1 TTTAATCCATAA-ACTTACAG
29447788 TTTAATCCATAAACTTACAG
1 TTTAATCCATAAACTTACAG
29447808 TTTA
1 TTTA
29447812 TTTAAAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 3 0.09
18 9 0.28
19 4 0.12
20 13 0.41
21 3 0.09
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.44
Consensus pattern (20 bp):
TTTAATCCATAAACTTACAG
Found at i:29447782 original size:38 final size:38
Alignment explanation
Indices: 29447740--29447816 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
29447730 CTAAATTGAG
*
29447740 ATACTTTCGATTTAATCCATAAACTTACAGTTTATTTA
1 ATACTTTCAATTTAATCCATAAACTTACAGTTTATTTA
29447778 ATACTTTCAATTTAATCCATAAACTTACAGTTTATTTA
1 ATACTTTCAATTTAATCCATAAACTTACAGTTTATTTA
29447816 A
1 A
29447817 AATTACTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (38 bp):
ATACTTTCAATTTAATCCATAAACTTACAGTTTATTTA
Found at i:29451627 original size:43 final size:43
Alignment explanation
Indices: 29451578--29451757 Score: 150
Period size: 43 Copynumber: 4.2 Consensus size: 43
29451568 GGCACTACAA
* *
29451578 TGCATCATCAGATAAACTGAAGGAA-ATATATTGGCACGCATAG
1 TGCATCATCAGATAAACCGAA-GAATATATACTGGCACGCATAG
** * * *
29451621 TGCATCATCAGATGTACCGAACAATGTATACTGGCACTCATAG
1 TGCATCATCAGATAAACCGAAGAATATATACTGGCACGCATAG
* * * * * *
29451664 TGTATCATCAAACAAGCTGAAGAA-ATTATACTGGCATGCATAG
1 TGCATCATCAGATAAACCGAAGAATA-TATACTGGCACGCATAG
* * * * * *
29451707 TGCATCATCGGATATACCGAAGAATGTATATTGAC-CTCATAG
1 TGCATCATCAGATAAACCGAAGAATATATACTGGCACGCATAG
29451749 TGCATCATC
1 TGCATCATC
29451758 GGACAAGTCG
Statistics
Matches: 104, Mismatches: 30, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
42 16 0.15
43 88 0.85
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (43 bp):
TGCATCATCAGATAAACCGAAGAATATATACTGGCACGCATAG
Found at i:29451711 original size:86 final size:86
Alignment explanation
Indices: 29451578--29451890 Score: 319
Period size: 86 Copynumber: 3.7 Consensus size: 86
29451568 GGCACTACAA
* * ** * * * * *
29451578 TGCATCATCAGATAAACTGAAGGAAATATATTGGCACGCATAGTGCATCATCAGATGTACCGAAC
1 TGCATCATCAGACAAGCTGAAACAATTATACTGGCATGCATAGTGCATCATCGGATGTACCGAAA
* *
29451643 AATGTATACTGGCACTCATAG
66 AATGTATATTGACACTCATAG
* * *
29451664 TGTATCATCAAACAAGCTGAAGA-AATTATACTGGCATGCATAGTGCATCATCGGATATACCGAA
1 TGCATCATCAGACAAGCTGAA-ACAATTATACTGGCATGCATAGTGCATCATCGGATGTACCGAA
*
29451728 GAATGTATATTGAC-CTCATAG
65 AAATGTATATTGACACTCATAG
* * * * *
29451749 TGCATCATCGGACAAG-TCGAAACAATTATACTGACATACATAGCGCATCATCGGATGTATCGAA
1 TGCATCATCAGACAAGCT-GAAACAATTATACTGGCATGCATAGTGCATCATCGGATGTACCGAA
*
29451813 AAATGTATATT-ATCACTCATAA
65 AAATGTATATTGA-CACTCATAG
* * * *** *
29451835 TGCATCATTAGACAAGCCGAAACAATTATATTGGCACATATAGTGTATCATCGGAT
1 TGCATCATCAGACAAGCTGAAACAATTATACTGGCATGCATAGTGCATCATCGGAT
29451891 AAATCAAAGC
Statistics
Matches: 189, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
84 3 0.02
85 70 0.37
86 116 0.61
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (86 bp):
TGCATCATCAGACAAGCTGAAACAATTATACTGGCATGCATAGTGCATCATCGGATGTACCGAAA
AATGTATATTGACACTCATAG
Found at i:29451812 original size:43 final size:42
Alignment explanation
Indices: 29451616--29451821 Score: 159
Period size: 43 Copynumber: 4.8 Consensus size: 42
29451606 TATTGGCACG
* * * * *
29451616 CATAGTGCATCATCAGATGTACCGAACAATGTATACTGGCACT
1 CATAGTGCATCATCGGATATATCGAAAAATGTATACTGACA-T
* ** * * *
29451659 CATAGTGTATCATCAAACA-AGCTGAAGAAAT-TATACTGGCAT
1 CATAGTGCATCATCGGATATATC-GAA-AAATGTATACTGACAT
* * * *
29451701 GCATAGTGCATCATCGGATATACCGAAGAATGTATATTGACCT
1 -CATAGTGCATCATCGGATATATCGAAAAATGTATACTGACAT
*
29451744 CATAGTGCATCATCGGACA-AGTCGAAACAAT-TATACTGACAT
1 CATAGTGCATCATCGGATATA-TCGAAA-AATGTATACTGACAT
* *
29451786 ACATAGCGCATCATCGGATGTATCGAAAAATGTATA
1 -CATAGTGCATCATCGGATATATCGAAAAATGTATA
29451822 TTATCACTCA
Statistics
Matches: 130, Mismatches: 23, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
41 1 0.01
42 40 0.31
43 83 0.64
44 6 0.05
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (42 bp):
CATAGTGCATCATCGGATATATCGAAAAATGTATACTGACAT
Found at i:29451840 original size:43 final size:42
Alignment explanation
Indices: 29451702--29451842 Score: 137
Period size: 43 Copynumber: 3.3 Consensus size: 42
29451692 TACTGGCATG
* *
29451702 CATAGTGCATCATCGGATATACCGAAGAATGTATATTGAC-CT
1 CATAGTGCATCATCGGATATATCGAAAAATGTATATT-ACACT
* *
29451744 CATAGTGCATCATCGGACA-AGTCGAAACAAT-TATACTGACA-T
1 CATAGTGCATCATCGGATATA-TCGAAA-AATGTATA-TTACACT
* *
29451786 ACATAGCGCATCATCGGATGTATCGAAAAATGTATATTATCACT
1 -CATAGTGCATCATCGGATATATCGAAAAATGTATATTA-CACT
*
29451830 CATAATGCATCAT
1 CATAGTGCATCAT
29451843 TAGACAAGCC
Statistics
Matches: 80, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
41 1 0.01
42 34 0.43
43 43 0.54
44 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (42 bp):
CATAGTGCATCATCGGATATATCGAAAAATGTATATTACACT
Found at i:29456996 original size:34 final size:34
Alignment explanation
Indices: 29456953--29457022 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
29456943 CGTTTTTTTA
*
29456953 AGTGTTAGGGTTTTGTTTATTTAAATTAGGGTTT
1 AGTGTTAGGGTTTTGTTTATTTAAAGTAGGGTTT
29456987 AGTGTTAGGGTTTTGTTTATTTAAAGTAGGGTTT
1 AGTGTTAGGGTTTTGTTTATTTAAAGTAGGGTTT
29457021 AG
1 AG
29457023 GGATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (34 bp):
AGTGTTAGGGTTTTGTTTATTTAAAGTAGGGTTT
Found at i:29458713 original size:18 final size:18
Alignment explanation
Indices: 29458690--29458725 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29458680 AATTTATGAG
*
29458690 ATTTTTTAAAATTTTTTA
1 ATTTTTTAAAATATTTTA
29458708 ATTTTTTAAAATATTTTA
1 ATTTTTTAAAATATTTTA
29458726 TTTAGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTTAAAATATTTTA
Found at i:29460227 original size:42 final size:42
Alignment explanation
Indices: 29460176--29460259 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
29460166 GGTACTCATC
29460176 GCCACTCACAGGGTATCTAAACGAGCCATCAGATTTGGTGTT
1 GCCACTCACAGGGTATCTAAACGAGCCATCAGATTTGGTGTT
29460218 GCCACTCACAGGGTATCTAAACGAGCCATCAGATTTGGTGTT
1 GCCACTCACAGGGTATCTAAACGAGCCATCAGATTTGGTGTT
29460260 TGAATGCTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (42 bp):
GCCACTCACAGGGTATCTAAACGAGCCATCAGATTTGGTGTT
Found at i:29460892 original size:25 final size:25
Alignment explanation
Indices: 29460858--29460907 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
29460848 CCACCCTAAG
29460858 AATAGCTAATAGAATTGACTTCTAC
1 AATAGCTAATAGAATTGACTTCTAC
29460883 AATAGCTAATAGAATTGACTTCTAC
1 AATAGCTAATAGAATTGACTTCTAC
29460908 CGAGTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (25 bp):
AATAGCTAATAGAATTGACTTCTAC
Found at i:29461160 original size:126 final size:126
Alignment explanation
Indices: 29460935--29461164 Score: 379
Period size: 126 Copynumber: 1.8 Consensus size: 126
29460925 CACTAACAAA
* *
29460935 GGTATTGGCATTTGTTATCGGTACACAGGAATCCTTAAATATTTTCCCAAATCTTCTGTCTGTTG
1 GGTATCGGCATTTGTTATCGGAACACAGGAATCCTTAAATATTTTCCCAAATCTTCTGTCTGTTG
29461000 AAAACCCAACTTGCTTGTAACATGACTCCACAATGATTCCAAACTTTGTCAAAAATGAATT
66 AAAACCCAACTTGCTTGTAACATGACTCCACAATGATTCCAAACTTTGTCAAAAATGAATT
* * * *
29461061 GGTATCGGCATTTGTTATTGGAATAGAGGAATCCTTAAATATTTTCCCAAATCTTCTGTTTGTTG
1 GGTATCGGCATTTGTTATCGGAACACAGGAATCCTTAAATATTTTCCCAAATCTTCTGTCTGTTG
* **
29461126 AAAACCCAACTTGCTTGTAACTTGACTCTTCAATGATTC
66 AAAACCCAACTTGCTTGTAACATGACTCCACAATGATTC
29461165 ACACGTGTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 95 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (126 bp):
GGTATCGGCATTTGTTATCGGAACACAGGAATCCTTAAATATTTTCCCAAATCTTCTGTCTGTTG
AAAACCCAACTTGCTTGTAACATGACTCCACAATGATTCCAAACTTTGTCAAAAATGAATT
Found at i:29464615 original size:35 final size:35
Alignment explanation
Indices: 29464529--29464627 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 35
29464519 GGTGACCGAT
*
29464529 AAAAATATAAGGATGACGAATGTGGCAACCCAACC
1 AAAAATATAAGGATGACGAATGTGGCGACCCAACC
* * * * * *
29464564 AGAAACATGAGAATGACGGATGTGGCGGCCCAACC
1 AAAAATATAAGGATGACGAATGTGGCGACCCAACC
* *
29464599 AAAAATATAAGGATGACGCATATGGCGAC
1 AAAAATATAAGGATGACGAATGTGGCGAC
29464628 TTGGCCAGAA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.14
Consensus pattern (35 bp):
AAAAATATAAGGATGACGAATGTGGCGACCCAACC
Found at i:29464684 original size:35 final size:35
Alignment explanation
Indices: 29464621--29464709 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 35
29464611 ATGACGCATA
* * *
29464621 TGGCGACTTGGCCAGAAACATAAAGATGATAGG-TG
1 TGGCGACTCGGCCAGAAATACAAAGATGAT-GGATG
* *
29464656 TGGCGACTCGGCCAGAAATACGAGGATGATGGATG
1 TGGCGACTCGGCCAGAAATACAAAGATGATGGATG
* * *
29464691 TGGTGAGTCGGCCAAAAAT
1 TGGCGACTCGGCCAGAAAT
29464710 GTAACACCCC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
34 2 0.04
35 43 0.96
ACGTcount: A:0.31, C:0.16, G:0.34, T:0.19
Consensus pattern (35 bp):
TGGCGACTCGGCCAGAAATACAAAGATGATGGATG
Found at i:29465094 original size:18 final size:17
Alignment explanation
Indices: 29465063--29465119 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
29465053 CTCATAACAA
29465063 CATAA-AACATGAGTTCG
1 CATAATAACA-GAGTTCG
*
29465080 CATAATAACACGAGTTCA
1 CATAATAACA-GAGTTCG
* *
29465098 CAAAATATCAGAGGTTCG
1 CATAATAACAGA-GTTCG
29465116 CATA
1 CATA
29465120 CTACATAAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.22
18 25 0.78
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (17 bp):
CATAATAACAGAGTTCG
Found at i:29469088 original size:23 final size:23
Alignment explanation
Indices: 29469051--29469101 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
29469041 GTGTGAGACA
29469051 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
29469074 TGTAATA-CCCAGAAAATTACTAC
1 TGTAATATCCC-GAAAATTACTAC
*
29469097 AGTAA
1 TGTAA
29469102 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:29475772 original size:35 final size:35
Alignment explanation
Indices: 29475733--29475814 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
29475723 AGGACAATGA
* * *
29475733 GTGTGGTTACCCAACCATAAACATGAA-GATGACGG
1 GTGTGGTAACCCAACCAGAAACA-CAATGATGACGG
**
29475768 GTGTGACAACCCAACCAGAAACACAATGATGACGG
1 GTGTGGTAACCCAACCAGAAACACAATGATGACGG
*
29475803 GTGTGGTGACCC
1 GTGTGGTAACCC
29475815 GATTAGAAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
34 2 0.05
35 36 0.95
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (35 bp):
GTGTGGTAACCCAACCAGAAACACAATGATGACGG
Found at i:29480888 original size:9 final size:9
Alignment explanation
Indices: 29480874--29480951 Score: 56
Period size: 9 Copynumber: 8.6 Consensus size: 9
29480864 ATTAAAATAT
*
29480874 AAATATTCA
1 AAATATTTA
29480883 AAATATTTTA
1 AAATA-TTTA
* *
29480893 AAAAATTAA
1 AAATATTTA
29480902 AAATATTTA
1 AAATATTTA
29480911 AAATA-TTA
1 AAATATTTA
29480919 AAAT-TTATA
1 AAATATT-TA
29480928 TAAA-ATTATA
1 -AAATATT-TA
29480938 AAA-ATTATA
1 AAATATT-TA
29480947 AAATA
1 AAATA
29480952 ATAATAACTT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
8 8 0.14
9 34 0.59
10 16 0.28
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (9 bp):
AAATATTTA
Found at i:29480906 original size:19 final size:18
Alignment explanation
Indices: 29480882--29480921 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
29480872 ATAAATATTC
29480882 AAAATATTTTAAAAAATTA
1 AAAATA-TTTAAAAAATTA
*
29480901 AAAATATTTAAAATATTA
1 AAAATATTTAAAAAATTA
29480919 AAA
1 AAA
29480922 TTTATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATATTTAAAAAATTA
Found at i:29480945 original size:19 final size:18
Alignment explanation
Indices: 29480899--29481134 Score: 109
Period size: 19 Copynumber: 12.8 Consensus size: 18
29480889 TTTAAAAAAT
*
29480899 TAAAAATATTTAAAA-TA
1 TAAAAATATATAAAATTA
*
29480916 TTAAAATTTATATAAAATTA
1 -TAAAA-ATATATAAAATTA
*
29480936 TAAAAAT-TATAAAATAA
1 TAAAAATATATAAAATTA
* *
29480953 TAATAACT-TGTAAATATTA
1 TAA-AAATATATAAA-ATTA
* *
29480972 TAAAAACATA-AAAACTA
1 TAAAAATATATAAAATTA
*
29480989 -ATAAAATCTA-AAAATTA
1 TA-AAAATATATAAAATTA
29481006 TAAAAA-ATTATAAAATTAA
1 TAAAAATA-TATAAAATT-A
*
29481025 TAAAACATATTTAAAATTTTA
1 TAAAA-ATATATAAAA--TTA
* *
29481046 TAAAAATGTATTAAAATTCT
1 TAAAAATATA-TAAAATT-A
*
29481066 TAAAAACT-TA-AAAATCA
1 TAAAAA-TATATAAAATTA
29481083 TAAAAA-ATAATTAAAA-TA
1 TAAAAATAT-A-TAAAATTA
* *
29481101 TTAAAATTGATATAAAATTG
1 -TAAAAAT-ATATAAAATTA
29481121 TAAAAAT-TATAAAA
1 TAAAAATATATAAAA
29481135 AATCATACAA
Statistics
Matches: 168, Mismatches: 25, Indels: 51
0.69 0.10 0.21
Matches are distributed among these distances:
16 2 0.01
17 47 0.28
18 32 0.19
19 48 0.29
20 22 0.13
21 15 0.09
22 2 0.01
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (18 bp):
TAAAAATATATAAAATTA
Found at i:29480955 original size:8 final size:8
Alignment explanation
Indices: 29480926--29481029 Score: 66
Period size: 9 Copynumber: 11.9 Consensus size: 8
29480916 TTAAAATTTA
29480926 TATAAAAT
1 TATAAAAT
29480934 TATAAAAAT
1 TAT-AAAAT
29480943 TATAAAAT
1 TATAAAAT
*
29480951 AATAATAACT
1 TATAA-AA-T
*
29480961 TGTAAATAT
1 TATAAA-AT
*
29480970 TATAAAAA
1 TATAAAAT
*
29480978 CATAAAAACT
1 TAT-AAAA-T
*
29480988 AATAAAAT
1 TATAAAAT
29480996 CTA-AAAAT
1 -TATAAAAT
29481004 TATAAAAAAT
1 TAT--AAAAT
29481014 TATAAAAT
1 TATAAAAT
29481022 TAATAAAA
1 T-ATAAAA
29481030 CATATTTAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
7 2 0.03
8 27 0.36
9 32 0.42
10 15 0.20
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (8 bp):
TATAAAAT
Found at i:29481050 original size:21 final size:20
Alignment explanation
Indices: 29481003--29481063 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
29480993 AATCTAAAAA
29481003 TTATAAAAA-ATTATAAAA-T
1 TTATAAAAATATT-TAAAATT
*
29481022 TAATAAAACATATTTAAAATT
1 TTATAAAA-ATATTTAAAATT
*
29481043 TTATAAAAATGTATTAAAATT
1 TTATAAAAATAT-TTAAAATT
29481064 CTTAAAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 7 0.20
20 9 0.26
21 19 0.54
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TTATAAAAATATTTAAAATT
Found at i:29481137 original size:10 final size:9
Alignment explanation
Indices: 29480893--29481135 Score: 112
Period size: 10 Copynumber: 26.6 Consensus size: 9
29480883 AAATATTTTA
29480893 AAAAATTA-
1 AAAAATTAT
29480901 AAAATATT-T
1 AAAA-ATTAT
29480910 -AAAA-TATT
1 AAAAATTA-T
*
29480918 AAAATTTAT
1 AAAAATTAT
29480927 ATAAAATTAT
1 A-AAAATTAT
29480937 AAAAATTAT
1 AAAAATTAT
*
29480946 -AAAATAAT
1 AAAAATTAT
* *
29480954 AATAACTTGT
1 AA-AAATTAT
*
29480964 AAATATTAT
1 AAAAATTAT
*
29480973 AAAAA-CAT
1 AAAAATTAT
*
29480981 AAAAACTA-
1 AAAAATTAT
*
29480989 ATAAAA-TCT
1 A-AAAATTAT
29480998 AAAAATTAT
1 AAAAATTAT
29481007 AAAAAATTAT
1 -AAAAATTAT
29481017 -AAAATTAAT
1 AAAAATT-AT
*
29481026 AAAACATATTT
1 AAAA-AT-TAT
*
29481037 AAAATTTTAT
1 AAAA-ATTAT
29481047 AAAAATGTAT
1 AAAAAT-TAT
* *
29481057 TAAAATTCTT
1 AAAAATT-AT
*
29481067 AAAAACT-T
1 AAAAATTAT
*
29481075 AAAAATCAT
1 AAAAATTAT
*
29481084 AAAAAATAAT
1 -AAAAATTAT
*
29481094 TAAAA-TAT
1 AAAAATTAT
*
29481102 TAAAATTGAT
1 AAAAATT-AT
*
29481112 ATAAAATTGT
1 A-AAAATTAT
29481122 AAAAATTAT
1 AAAAATTAT
29481131 AAAAA
1 AAAAA
29481136 ATCATACAAA
Statistics
Matches: 179, Mismatches: 31, Indels: 49
0.69 0.12 0.19
Matches are distributed among these distances:
6 1 0.01
7 1 0.01
8 47 0.26
9 55 0.31
10 60 0.34
11 14 0.08
12 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29481879 original size:29 final size:29
Alignment explanation
Indices: 29481846--29481910 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
29481836 TATATATTTA
*
29481846 ATAATTTATTAAAATTTATTA-GTTTTTTT
1 ATAATTTATTAAAATTT-TTATGATTTTTT
* *
29481875 ATAATTTTTTAAAGTTTTTATGATTTTTT
1 ATAATTTATTAAAATTTTTATGATTTTTT
*
29481904 ATCATTT
1 ATAATTT
29481911 CTATAAATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.10
29 28 0.90
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (29 bp):
ATAATTTATTAAAATTTTTATGATTTTTT
Found at i:29481882 original size:10 final size:10
Alignment explanation
Indices: 29481869--29481910 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
29481859 ATTTATTAGT
29481869 TTTTTTATAA
1 TTTTTTATAA
29481879 TTTTTTA-AA
1 TTTTTTATAA
* *
29481888 GTTTTTATGA
1 TTTTTTATAA
*
29481898 TTTTTTATCA
1 TTTTTTATAA
29481908 TTT
1 TTT
29481911 CTATAAATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:29481983 original size:9 final size:9
Alignment explanation
Indices: 29481925--29481998 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 9
29481915 AAATGTATGT
29481925 TAATTTTAA
1 TAATTTTAA
*
29481934 TAAATTTAA
1 TAATTTTAA
*
29481943 TAAATTTAA
1 TAATTTTAA
29481952 T-ATTTT-A
1 TAATTTTAA
*
29481959 TACTTTT-A
1 TAATTTTAA
*
29481967 TGATTTTTAA
1 T-AATTTTAA
29481977 TAATTTTTAA
1 TAA-TTTTAA
*
29481987 TAATTTTTA
1 TAATTTTAA
29481996 TAA
1 TAA
29481999 AATTTTAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
7 2 0.04
8 10 0.18
9 32 0.58
10 11 0.20
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (9 bp):
TAATTTTAA
Found at i:29481984 original size:10 final size:10
Alignment explanation
Indices: 29481969--29482013 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
29481959 TACTTTTATG
29481969 ATTTTTAATA
1 ATTTTTAATA
29481979 ATTTTTAATA
1 ATTTTTAATA
*
29481989 ATTTTTATAAA
1 ATTTTTA-ATA
*
29482000 ATTTTAAAT-
1 ATTTTTAATA
29482009 ATTTT
1 ATTTT
29482014 AAACATGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 5 0.16
10 18 0.58
11 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:29489036 original size:30 final size:30
Alignment explanation
Indices: 29489002--29489070 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
29488992 AATTAATTCG
29489002 GTTAACCGACCGATTAACTGAATTCGATCA
1 GTTAACCGACCGATTAACTGAATTCGATCA
29489032 GTTAACCGACCGATTAACTGAATTCGATCA
1 GTTAACCGACCGATTAACTGAATTCGATCA
29489062 GTTAACCGA
1 GTTAACCGA
29489071 ATTAATTTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (30 bp):
GTTAACCGACCGATTAACTGAATTCGATCA
Found at i:29489198 original size:18 final size:18
Alignment explanation
Indices: 29489175--29489210 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29489165 GAAAAAAAAG
29489175 TTTATATTATATTATAAA
1 TTTATATTATATTATAAA
29489193 TTTATATTATATTATAAA
1 TTTATATTATATTATAAA
29489211 AAGGATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATATTATATTATAAA
Found at i:29492266 original size:4 final size:4
Alignment explanation
Indices: 29492257--29492298 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
29492247 AAAAACTAAA
29492257 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
29492299 GTGTGTGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:29497005 original size:27 final size:27
Alignment explanation
Indices: 29496967--29497020 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
29496957 TTTGGGGTTA
*
29496967 GTAGAAATAACTAGTGTTTATAAGTCT
1 GTAGAAATAACTAGTGCTTATAAGTCT
29496994 GTAGAAATAACTAGTGCTTATAAGTCT
1 GTAGAAATAACTAGTGCTTATAAGTCT
29497021 ACTAGTAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (27 bp):
GTAGAAATAACTAGTGCTTATAAGTCT
Found at i:29513826 original size:50 final size:51
Alignment explanation
Indices: 29513714--29513850 Score: 163
Period size: 50 Copynumber: 2.7 Consensus size: 51
29513704 GGTAAAGAGG
* * **
29513714 TCCCATGTAAGACCATGTCTGGAACATGGCGTTGGCACCAAGATAAGAGGTC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACC-AGATAAGAGAAC
* *
29513766 TCCC--GTAAGACCATGTTTGGGACATGGCATTGGCACC-GATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAGATAAGAGAAC
* * *
29513814 TCCCATGCAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
29513851 GTACTGAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 12 0.16
50 57 0.78
52 4 0.05
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (51 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAGATAAGAGAAC
Found at i:29515195 original size:26 final size:26
Alignment explanation
Indices: 29515159--29515211 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
29515149 TTAAGTCAAG
29515159 TAACGCCTCATGATCGACTCCGGCAA
1 TAACGCCTCATGATCGACTCCGGCAA
*
29515185 TAACGCCTCATGATCGACTCTGGCAA
1 TAACGCCTCATGATCGACTCCGGCAA
29515211 T
1 T
29515212 GGTATTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (26 bp):
TAACGCCTCATGATCGACTCCGGCAA
Found at i:29517146 original size:19 final size:19
Alignment explanation
Indices: 29517122--29517160 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
29517112 TGCAGGAATT
29517122 AACTGATAAAGGTTTTGCA
1 AACTGATAAAGGTTTTGCA
*
29517141 AACTGATTAAGGTTTTGCA
1 AACTGATAAAGGTTTTGCA
29517160 A
1 A
29517161 GGCCTAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (19 bp):
AACTGATAAAGGTTTTGCA
Found at i:29522328 original size:28 final size:27
Alignment explanation
Indices: 29522267--29522328 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 27
29522257 TTTGAGTTTA
*
29522267 AGGTTTAAGAGTTTGGAGGTTGGGTTT
1 AGGTTTAAGAGTTTGGAGGTTGGGTTC
29522294 AGTGTTTAATGA-TTTGG-GGTTATGGGTTC
1 AG-GTTTAA-GAGTTTGGAGG-T-TGGGTTC
29522323 AGGTTT
1 AGGTTT
29522329 GGGGTTGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
27 4 0.13
28 16 0.53
29 10 0.33
ACGTcount: A:0.18, C:0.02, G:0.37, T:0.44
Consensus pattern (27 bp):
AGGTTTAAGAGTTTGGAGGTTGGGTTC
Found at i:29528342 original size:5 final size:6
Alignment explanation
Indices: 29528326--29528350 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29528316 GTAGAAATGC
29528326 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
29528351 GGGGGGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:29528453 original size:20 final size:19
Alignment explanation
Indices: 29528405--29528453 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
29528395 AAAATAAAAT
*
29528405 AAAATAAAAATAGATTCAA
1 AAAATAAAAATAAATTCAA
* *
29528424 AAATACAAAAATAAATTTAA
1 AAA-ATAAAAATAAATTCAA
29528444 GAAAATAAAA
1 -AAAATAAAA
29528454 CAAATGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAATAAAAATAAATTCAA
Found at i:29535100 original size:3 final size:3
Alignment explanation
Indices: 29535092--29535122 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29535082 AAAATTACAA
29535092 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
29535123 CTAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29539849 original size:71 final size:72
Alignment explanation
Indices: 29539743--29539880 Score: 188
Period size: 71 Copynumber: 1.9 Consensus size: 72
29539733 CCAAATGAAT
* * * *
29539743 ATTAAAACTAAATAAAATCTATTTGGGGATTTATTCCTGCCGTTTAACAAATTTTATTCGATTTT
1 ATTAAAACTAAATAAAATCCATTTGGGGATTTATTCCCGCCGTTCAACAAATTTTATTCCATTTT
29539808 TTTCCAA
66 TTTCCAA
* * * * *
29539815 ATTAAAAGTAAAT-AAATCCGTTTTGGGATTTATTCCCGCTGTTCAACGAATTTTATTCCATTTT
1 ATTAAAACTAAATAAAATCCATTTGGGGATTTATTCCCGCCGTTCAACAAATTTTATTCCATTTT
29539879 TT
66 TT
29539881 ATTATTTCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
71 45 0.79
72 12 0.21
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (72 bp):
ATTAAAACTAAATAAAATCCATTTGGGGATTTATTCCCGCCGTTCAACAAATTTTATTCCATTTT
TTTCCAA
Found at i:29540020 original size:89 final size:89
Alignment explanation
Indices: 29539815--29540395 Score: 472
Period size: 89 Copynumber: 6.7 Consensus size: 89
29539805 TTTTTTCCAA
* * * * * *
29539815 ATTAAAAGT-AAAT-AAATCCGTTTTGGGATTTATTCCCGCTGTTCAAC-GAATTTTATTCC-AT
1 ATTAAAATTAAAATAAAATCTGTTTCGAGATTTATTCCTGCCGTTCAACAG-ATTTTATTCCAAT
* *
29539876 TTT--TTATTATTT-C-TAAACGAGAA
65 TTTGATT-TTATTTCCAAAAACGAG-T
* * * * * * *
29539899 ATT-AAAGTCAAATAAAATTTGTTTCAAAATTTATTCCTGTCGTTCAATAGATTTTATTCCAATT
1 ATTAAAATTAAAATAAAATCTGTTTCGAGATTTATTCCTGCCGTTCAACAGATTTTATTCCAATT
29539963 TTGATTTTATTTCCAAAAACGAGT
66 TTGATTTTATTTCCAAAAACGAGT
* * * *
29539987 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCAGTCGTTCAACGGATTTTATTCCAATT
1 ATTAAAATTAAAATAAAATCTGTTTCGAGATTTATTCCTGCCGTTCAACAGATTTTATTCCAATT
* *
29540052 TTCATTTTATTTTCAAAAACGAGT
66 TTGATTTTATTTCCAAAAACGAGT
*
29540076 ATTAAAATTAAAATAAAATCTGTTTCG-GAATTTATTCAC-GCTGTTCAAC-GAATTTTATTCCA
1 ATTAAAATTAAAATAAAATCTGTTTCGAG-ATTTATTC-CTGCCGTTCAACAG-ATTTTATTCCA
* *
29540138 ATTTTGGTTTTATTTCCAAAAATGAGT
63 ATTTTGATTTTATTTCCAAAAACGAGT
* * * *
29540165 ATTAAAATAAAAATAAAATCTGTTTCGAGATTTATT-CTCACCGTTCAACGGA-TTTATTAC-AT
1 ATTAAAATTAAAATAAAATCTGTTTCGAGATTTATTCCT-GCCGTTCAACAGATTTTATTCCAAT
* * * *
29540227 TTTGATTTTGTTGCCAAAAATGAGAA
65 TTTGATTTTATTTCCAAAAACGAG-T
* * * * * **
29540253 ATTAAAATT-AAATAAAATTTGTTCCAAGATTTATTCATGCCGTTTAACAAGATTTTATT-TGAT
1 ATTAAAATTAAAATAAAATCTGTTTCGAGATTTATTCCTGCCGTTCAAC-AGATTTTATTCCAAT
* * *
29540316 TTT-ATTTTGTTTCTAAATTA-GA--
65 TTTGATTTTATTTCCAAA-AACGAGT
* * * *
29540338 ATT-AAATT-AAATAAAATCTGTTTCAAGATATATT-CTCGTCGTTTAACAAGATTTTATT
1 ATTAAAATTAAAATAAAATCTGTTTCGAGATTTATTCCT-GCCGTTCAAC-AGATTTTATT
29540396 TTGTTTCCAA
Statistics
Matches: 420, Mismatches: 54, Indels: 46
0.81 0.10 0.09
Matches are distributed among these distances:
83 6 0.01
84 55 0.13
85 37 0.09
86 6 0.01
87 61 0.15
88 40 0.10
89 212 0.50
90 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (89 bp):
ATTAAAATTAAAATAAAATCTGTTTCGAGATTTATTCCTGCCGTTCAACAGATTTTATTCCAATT
TTGATTTTATTTCCAAAAACGAGT
Found at i:29540110 original size:178 final size:175
Alignment explanation
Indices: 29539815--29540289 Score: 556
Period size: 178 Copynumber: 2.7 Consensus size: 175
29539805 TTTTTTCCAA
* * * * *
29539815 ATTAAAAGT-AAAT-AAATCCGTTTTGGGATTTATTCCCGCTGTTCAACGAATTTTATTCCATTT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCAGC-GTTCAACGGATTTTATTCCATTT
* * *
29539878 T-TTATTA-TTTC-TAAACGAGAAATTAAAGTCAAATAAAATTTGTTTCAAAATTTATTC-CTG-
65 TATT-TTATTTTCAAAAACGAGAAATTAAAATTAAATAAAATTTGTTTCAAAATTTATTCAC-GC
29539938 TCGTTCAATAG-ATTTTATTCCAATTTTGATTTTATTTCCAAAAACGAGT
128 T-GTTCAA-AGAATTTTATTCCAATTTTGATTTTATTTCCAAAAACGAGT
29539987 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCAGTCGTTCAACGGATTTTATTCCAATT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCAG-CGTTCAACGGATTTTATTCC-ATT
* * **
29540052 TTCATTTTATTTTCAAAAACGAG-TATTAAAATTAAAATAAAATCTGTTTCGGAATTTATTCACG
64 TT-ATTTTATTTTCAAAAACGAGAAATTAAAATT-AAATAAAATTTGTTTCAAAATTTATTCACG
* * *
29540116 CTGTTCAACGAATTTTATTCCAATTTTGGTTTTATTTCCAAAAATGAGT
127 CTGTTCAAAGAATTTTATTCCAATTTTGATTTTATTTCCAAAAACGAGT
* * * *
29540165 ATTAAAATAAAAATAAAATCTGTTTCGAGATTTATTCTCACCGTTCAACGGA-TTTATTACATTT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTC-CAGCGTTCAACGGATTTTATTCCATTT
* ** * * *
29540229 TGATTTTGTTGCCAAAAATGAGAAATTAAAATTAAATAAAATTTGTTCCAAGATTTATTCA
65 T-ATTTTATTTTCAAAAACGAGAAATTAAAATTAAATAAAATTTGTTTCAAAATTTATTCA
29540290 TGCCGTTTAA
Statistics
Matches: 259, Mismatches: 30, Indels: 24
0.83 0.10 0.08
Matches are distributed among these distances:
172 8 0.03
173 4 0.02
174 40 0.15
175 6 0.02
176 47 0.18
177 30 0.12
178 120 0.46
179 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (175 bp):
ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCAGCGTTCAACGGATTTTATTCCATTTT
ATTTTATTTTCAAAAACGAGAAATTAAAATTAAATAAAATTTGTTTCAAAATTTATTCACGCTGT
TCAAAGAATTTTATTCCAATTTTGATTTTATTTCCAAAAACGAGT
Found at i:29540365 original size:84 final size:83
Alignment explanation
Indices: 29540175--29540572 Score: 385
Period size: 84 Copynumber: 4.8 Consensus size: 83
29540165 ATTAAAATAA
* * * * **
29540175 AAATAAAATCTGTTTCGAGATTTATTCTCACCGTTCAAC-GGA-TTTATTACATTTTGATTTTGT
1 AAATAAAATCTGTTTCAAGATTTATTCT-GCCGTTTAACAAGATTTTATTTGATTTT-ATTTTGT
* *
29540238 TGCCAAAAATGAGAAATTAAAATT
64 TTCC--AAATTAG-AATT-AAATT
* *
29540262 AAATAAAATTTGTTCCAAGATTTATTCATGCCGTTTAACAAGATTTTATTTGATTTTATTTTGTT
1 AAATAAAATCTGTTTCAAGATTTATTC-TGCCGTTTAACAAGATTTTATTTGATTTTATTTTGTT
*
29540327 TCTAAATTAGAATTAAATT
65 TCCAAATTAGAATTAAATT
* *
29540346 AAATAAAATCTGTTTCAAGATATATTCTCGTCGTTTAAC---A----A---GATTTTATTTTGTT
1 AAATAAAATCTGTTTCAAGATTTATTCT-GCCGTTTAACAAGATTTTATTTGATTTTATTTTGTT
29540401 TCCAAATTAGAATTAAATT
65 TCCAAATTAGAATTAAATT
** * * * *
29540420 AAATAAAATCTGTTTTGAGATATATCCCTGCCGTTTAA-AAGGATTTTATTTAATTTAATTTTGT
1 AAATAAAATCTGTTTCAAGATTTAT-TCTGCCGTTTAACAA-GATTTTATTTGATTTTATTTTGT
29540484 TTCCAAATTAGAATTAAATT
64 TTCCAAATTAGAATTAAATT
* * * *
29540504 AAATAAAATCTGTTTCAAGATTT-TCCCT-CCGTTTAACAAGATTTTATTCGATATTGTTTTGTT
1 AAATAAAATCTGTTTCAAGATTTAT-TCTGCCGTTTAACAAGATTTTATTTGATTTTATTTTGTT
29540567 TCCAAA
65 TCCAAA
29540573 CAAAAACGTA
Statistics
Matches: 264, Mismatches: 30, Indels: 39
0.79 0.09 0.12
Matches are distributed among these distances:
74 63 0.24
75 2 0.01
77 2 0.01
81 2 0.01
82 33 0.12
83 8 0.03
84 89 0.34
85 4 0.02
86 6 0.02
87 32 0.12
88 12 0.05
89 11 0.04
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (83 bp):
AAATAAAATCTGTTTCAAGATTTATTCTGCCGTTTAACAAGATTTTATTTGATTTTATTTTGTTT
CCAAATTAGAATTAAATT
Found at i:29540395 original size:74 final size:73
Alignment explanation
Indices: 29540313--29540551 Score: 277
Period size: 74 Copynumber: 3.1 Consensus size: 73
29540303 GATTTTATTT
*
29540313 GATTTTATTTTGTTTCTAAATTAGAATTAAATTAAATAAAATCTGTTTCAAGATATATTCTCGTC
1 GATTTTATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAAGATATATTC-CGTC
29540378 GTTTAACAA
65 GTTTAACAA
** * *
29540387 GATTTTATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTTGAGATATATCCCTGCC
1 GATTTTATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAAGATATATTCC-GTC
29540452 GTTTAA-AA
65 GTTTAACAA
29540460 GGATTTTATTTAATTTAATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAAGAT
1 -G-----A--T--TTT-ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAAGAT
*
29540525 -T-TTCCCTCCGTTTAACAA
55 ATATTCCGT-CGTTTAACAA
29540543 GATTTTATT
1 GATTTTATT
29540552 CGATATTGTT
Statistics
Matches: 141, Mismatches: 10, Indels: 30
0.78 0.06 0.17
Matches are distributed among these distances:
72 3 0.02
73 6 0.04
74 65 0.46
75 1 0.01
77 1 0.01
79 1 0.01
81 1 0.01
82 11 0.08
83 6 0.04
84 46 0.33
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (73 bp):
GATTTTATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAAGATATATTCCGTCG
TTTAACAA
Found at i:29540590 original size:82 final size:81
Alignment explanation
Indices: 29540391--29540651 Score: 233
Period size: 82 Copynumber: 3.1 Consensus size: 81
29540381 TAACAAGATT
** * * * *
29540391 TTATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTTGAGATATATCCCTGCCGTTT
1 TTATTTTGTTTCCAAACAAAAAGTAAATCAAATAAAATCTGTTTTGAGAT-TTTCCCT-CCGTTT
*
29540456 AAAAGGATTTTATTTAAT-
64 AAAA-GATTTTATTTGATA
** * * * **
29540474 TTAATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAAGATTTTCCCTCCGTTTA
1 TT-ATTTTGTTTCCAAACAAAAAGTAAATCAAATAAAATCTGTTTTGAGATTTTCCCTCCGTTTA
*
29540539 ACAAGATTTTATTCGATA
65 A-AAGATTTTATTTGATA
* *
29540557 TTGTTTTGTTTCCAAACAAAAACGT-AATCAAAT-AATTCTGTTTTGAGATTTATTCCCGT-CGT
1 TTATTTTGTTTCCAAACAAAAA-GTAAATCAAATAAAATCTGTTTTGAGA-TT-TTCCC-TCCGT
*
29540619 TTAATAGATTTTATTTTGATA
62 TTAAAAGATTTTA-TTTGATA
*
29540640 TAATTTTGTTTC
1 TTATTTTGTTTC
29540652 AAGATTTAAT
Statistics
Matches: 152, Mismatches: 18, Indels: 16
0.82 0.10 0.09
Matches are distributed among these distances:
81 12 0.08
82 52 0.34
83 41 0.27
84 47 0.31
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (81 bp):
TTATTTTGTTTCCAAACAAAAAGTAAATCAAATAAAATCTGTTTTGAGATTTTCCCTCCGTTTAA
AAGATTTTATTTGATA
Found at i:29543905 original size:31 final size:30
Alignment explanation
Indices: 29543870--29543929 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29543860 GGAGGTGGGA
*
29543870 TGGGAAGGAAATAAAAGTTTTGGGGGAAAAG
1 TGGG-AGGAAATAAAAATTTTGGGGGAAAAG
* *
29543901 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGGAAATAAAAATTTTGGGGGAAAA
29543930 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (30 bp):
TGGGAGGAAATAAAAATTTTGGGGGAAAAG
Found at i:29544165 original size:18 final size:18
Alignment explanation
Indices: 29544142--29544178 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29544132 TATAGTTTGA
*
29544142 TATTTGAATTATTCGAAT
1 TATTTGAATTATTCAAAT
*
29544160 TATTTGAGTTATTCAAAT
1 TATTTGAATTATTCAAAT
29544178 T
1 T
29544179 CGAAAACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TATTTGAATTATTCAAAT
Found at i:29545264 original size:20 final size:20
Alignment explanation
Indices: 29545241--29545280 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29545231 TATTTGGTTC
* *
29545241 TAATCAATTTGATTTGATTT
1 TAATCAAATTGATTCGATTT
29545261 TAATCAAATTGATTCGATTT
1 TAATCAAATTGATTCGATTT
29545281 CCCCTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (20 bp):
TAATCAAATTGATTCGATTT
Found at i:29545302 original size:21 final size:23
Alignment explanation
Indices: 29545278--29545321 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29545268 ATTGATTCGA
29545278 TTTCCCCTT-TA-ATGCATATTT
1 TTTCCCCTTATACATGCATATTT
* *
29545299 TTTCTCCTTATACATGGATATTT
1 TTTCCCCTTATACATGCATATTT
29545322 CCAAAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTCCCCTTATACATGCATATTT
Found at i:29548001 original size:22 final size:22
Alignment explanation
Indices: 29547973--29548116 Score: 207
Period size: 22 Copynumber: 6.5 Consensus size: 22
29547963 CAACCAAATC
*
29547973 GCTCTCATGTTTCACGTACTAA
1 GCTCTCATGTTTAACGTACTAA
29547995 GCTCTCATGTTTAACGTACTAA
1 GCTCTCATGTTTAACGTACTAA
*
29548017 GCTCTCATGTTTAACGAACTAA
1 GCTCTCATGTTTAACGTACTAA
* * **
29548039 ACCCTCATGGCTAACGTACTAA
1 GCTCTCATGTTTAACGTACTAA
**
29548061 GCTCTCATGGCTAACGTACTAA
1 GCTCTCATGTTTAACGTACTAA
*
29548083 GCTCTCATGTTTCACGTACTAA
1 GCTCTCATGTTTAACGTACTAA
29548105 GCTCTCATGTTT
1 GCTCTCATGTTT
29548117 GAACAATAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 110 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (22 bp):
GCTCTCATGTTTAACGTACTAA
Found at i:29550273 original size:40 final size:40
Alignment explanation
Indices: 29550226--29550399 Score: 197
Period size: 40 Copynumber: 4.3 Consensus size: 40
29550216 GAATGAATTT
* * *
29550226 ACATATGTGCCCCTATTTGTACTTCGGTACCCTTGAATGC
1 ACATACGTGCCCCTATTTGTACTTTGGTACCCCTGAATGC
* * * *
29550266 TCATATGTGCCCTTGTTTGTACTTTGGTACCCCTGAATGC
1 ACATACGTGCCCCTATTTGTACTTTGGTACCCCTGAATGC
* * *
29550306 ACATACATGCCCATGTTTGTACTTTGGTACCCCTGAATGC
1 ACATACGTGCCCCTATTTGTACTTTGGTACCCCTGAATGC
* * *
29550346 ACATACGTCCCCCTGA-ATGTACTTTGATACCCCTGAATGC
1 ACATACGTGCCCCT-ATTTGTACTTTGGTACCCCTGAATGC
* *
29550386 ACTTACATGCCCCT
1 ACATACGTGCCCCT
29550400 GTTTATCCTC
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
40 115 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (40 bp):
ACATACGTGCCCCTATTTGTACTTTGGTACCCCTGAATGC
Found at i:29550367 original size:80 final size:80
Alignment explanation
Indices: 29550241--29550403 Score: 227
Period size: 80 Copynumber: 2.0 Consensus size: 80
29550231 TGTGCCCCTA
* * * * * ** *
29550241 TTTGTACTTCGGTACCCTTGAATGCTCATATGTGCCCTTGTTTGTACTTTGGTACCCCTGAATGC
1 TTTGTACTTCGGTACCCCTGAATGCACATACGTCCCCCTGAATGTACTTTGATACCCCTGAATGC
29550306 ACATACATGCCCATG
66 ACATACATGCCCATG
*
29550321 TTTGTACTTTGGTACCCCTGAATGCACATACGTCCCCCTGAATGTACTTTGATACCCCTGAATGC
1 TTTGTACTTCGGTACCCCTGAATGCACATACGTCCCCCTGAATGTACTTTGATACCCCTGAATGC
* *
29550386 ACTTACATGCCCCTG
66 ACATACATGCCCATG
29550401 TTT
1 TTT
29550404 ATCCTCTAGT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (80 bp):
TTTGTACTTCGGTACCCCTGAATGCACATACGTCCCCCTGAATGTACTTTGATACCCCTGAATGC
ACATACATGCCCATG
Found at i:29550378 original size:20 final size:19
Alignment explanation
Indices: 29550326--29550389 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
29550316 CCATGTTTGT
29550326 ACTTTGGTACCCCTGAATGC
1 ACTTT-GTACCCCTGAATGC
** * *
29550346 ACATACGTCCCCCTGAATGT
1 AC-TTTGTACCCCTGAATGC
29550366 ACTTTGATACCCCTGAATGC
1 ACTTTG-TACCCCTGAATGC
29550386 ACTT
1 ACTT
29550390 ACATGCCCCT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 2 0.06
20 31 0.91
21 1 0.03
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (19 bp):
ACTTTGTACCCCTGAATGC
Found at i:29550398 original size:20 final size:20
Alignment explanation
Indices: 29550333--29550400 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
29550323 TGTACTTTGG
* *
29550333 TACCCCTGAATGCACATACG
1 TACCCCTGAATGCACTTACA
* * **
29550353 TCCCCCTGAATGTACTTTGA
1 TACCCCTGAATGCACTTACA
29550373 TACCCCTGAATGCACTTACA
1 TACCCCTGAATGCACTTACA
*
29550393 TGCCCCTG
1 TACCCCTG
29550401 TTTATCCTCT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (20 bp):
TACCCCTGAATGCACTTACA
Found at i:29553884 original size:25 final size:25
Alignment explanation
Indices: 29553813--29553885 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
29553803 TCCTGTACAT
* * *
29553813 GTATGCTTATACGAGCTGTGAATCA
1 GTATGCTCACACGAGCTGTAAATCA
* *
29553838 GTATGCTCACTCGAGCTATAAATCA
1 GTATGCTCACACGAGCTGTAAATCA
* *
29553863 GTATGCTCTCACGAACTGTAAAT
1 GTATGCTCACACGAGCTGTAAAT
29553886 TGGAATGCTC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATCA
Found at i:29554800 original size:20 final size:20
Alignment explanation
Indices: 29554775--29554826 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
29554765 AAAGATGATA
29554775 TTAATTTACTTTTAATTTAC
1 TTAATTTACTTTTAATTTAC
* *
29554795 TTAATTTGTCATTT-ATTTAC
1 TTAATTT-ACTTTTAATTTAC
29554815 -TAA-TTACTTTTA
1 TTAATTTACTTTTA
29554827 TAACCTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
17 4 0.15
18 2 0.08
19 3 0.12
20 13 0.50
21 4 0.15
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAATTTACTTTTAATTTAC
Found at i:29556831 original size:16 final size:16
Alignment explanation
Indices: 29556810--29556842 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29556800 TTTTGTTATC
*
29556810 GTATTAACTTAATTTA
1 GTATTAACTGAATTTA
29556826 GTATTAACTGAATTTA
1 GTATTAACTGAATTTA
29556842 G
1 G
29556843 CTAACTCGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (16 bp):
GTATTAACTGAATTTA
Found at i:29560877 original size:40 final size:40
Alignment explanation
Indices: 29560826--29561012 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
29560816 TATATATGTC
* * *
29560826 CCCCCGTTTGTACTTCGGTACCCTTGAATGCACACACATG
1 CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATG
*
29560866 CCCCTGTTTGTACTTCAGTACCCCTGAATGCACATACATG
1 CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATG
* * **
29560906 CCCCTGTTTGTACTTTGGTACCCCTGAATGCATATACACA
1 CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATG
* * * * *
29560946 CCCCTGATTGTACTTCAGT--CCCTGACTGCACTTATATG
1 CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATG
* * * * *
29560984 CCCTTGTTTATACCTCGGTAACTCTGAAT
1 CCCCTGTTTGTACTTCGGTACCCCTGAAT
29561013 CATATAGTAT
Statistics
Matches: 120, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
38 27 0.22
40 93 0.77
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.32
Consensus pattern (40 bp):
CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATG
Found at i:29560891 original size:20 final size:20
Alignment explanation
Indices: 29560866--29560931 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
29560856 CACACACATG
29560866 CCCCTGTTTGTACTTCAGTA
1 CCCCTGTTTGTACTTCAGTA
** * * *
29560886 CCCCTGAATGCACATACA-TG
1 CCCCTGTTTGTAC-TTCAGTA
**
29560906 CCCCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTCAGTA
29560926 CCCCTG
1 CCCCTG
29560932 AATGCATATA
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.88
21 3 0.09
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCAGTA
Found at i:29561011 original size:78 final size:78
Alignment explanation
Indices: 29560866--29561018 Score: 191
Period size: 78 Copynumber: 1.9 Consensus size: 78
29560856 CACACACATG
* * * * *
29560866 CCCCTGTTTGTACTTCAGTACCCCTGAATGCACATACATGCCCCTGTTTGTACTTTGGTACCCCT
1 CCCCTGATTGTACTTCAGTA-CCCTGAATGCACATACATGCCCCTGTTTATACCTCGGTAACCCT
29560931 GAATGCATATACACA
65 GAAT-CATATACACA
* * * * *
29560946 CCCCTGATTGTACTTCAGT-CCCTGACTGCACTTATATGCCCTTGTTTATACCTCGGTAACTCTG
1 CCCCTGATTGTACTTCAGTACCCTGAATGCACATACATGCCCCTGTTTATACCTCGGTAACCCTG
29561010 AATCATATA
66 AATCATATA
29561019 GTATAGGATT
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
77 6 0.10
78 39 0.62
80 18 0.29
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.33
Consensus pattern (78 bp):
CCCCTGATTGTACTTCAGTACCCTGAATGCACATACATGCCCCTGTTTATACCTCGGTAACCCTG
AATCATATACACA
Found at i:29577573 original size:21 final size:21
Alignment explanation
Indices: 29577547--29577611 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
29577537 TGCTATTTTT
29577547 TATATATTATATAATTTATAA
1 TATATATTATATAATTTATAA
*
29577568 TATATA-TAAATTAAATTTATAA
1 TATATATTATA-T-AATTTATAA
* *
29577590 TAGTATATAATATTA-TTATAA
1 TA-TATATTATATAATTTATAA
29577611 T
1 T
29577612 GTAAACATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 3 0.08
21 14 0.39
22 12 0.33
23 5 0.14
24 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TATATATTATATAATTTATAA
Found at i:29577587 original size:22 final size:24
Alignment explanation
Indices: 29577559--29577604 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
29577549 TATATTATAT
29577559 AATTTATAATA-TATATAA-ATTA
1 AATTTATAATAGTATATAATATTA
29577581 AATTTATAATAGTATATAATATTA
1 AATTTATAATAGTATATAATATTA
29577605 TTATAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 7 0.32
24 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AATTTATAATAGTATATAATATTA
Found at i:29579770 original size:16 final size:16
Alignment explanation
Indices: 29579751--29579782 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29579741 ACTTTGGGAG
29579751 TTAGTTTCTTTGTATA
1 TTAGTTTCTTTGTATA
29579767 TTAGTTTCTTTGTATA
1 TTAGTTTCTTTGTATA
29579783 AGATTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (16 bp):
TTAGTTTCTTTGTATA
Found at i:29579791 original size:15 final size:15
Alignment explanation
Indices: 29579752--29579792 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
29579742 CTTTGGGAGT
29579752 TAGTTTCTTTGTATA
1 TAGTTTCTTTGTATA
29579767 TTAGTTTCTTTGTATA
1 -TAGTTTCTTTGTATA
29579783 -AGATTTCTTT
1 TAG-TTTCTTT
29579793 CTTGTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.08
15 7 0.29
16 15 0.62
ACGTcount: A:0.20, C:0.07, G:0.12, T:0.61
Consensus pattern (15 bp):
TAGTTTCTTTGTATA
Found at i:29587232 original size:27 final size:27
Alignment explanation
Indices: 29587201--29587257 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
29587191 TATGGGTTCC
29587201 TCAGTATACGTCAAATTAGGCTGAAAT
1 TCAGTATACGTCAAATTAGGCTGAAAT
29587228 TCAGTATACGTCAAATTAGGCTGAAAT
1 TCAGTATACGTCAAATTAGGCTGAAAT
29587255 TCA
1 TCA
29587258 ATCTCACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (27 bp):
TCAGTATACGTCAAATTAGGCTGAAAT
Found at i:29601148 original size:14 final size:14
Alignment explanation
Indices: 29601129--29601158 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29601119 GCCAGTATTC
29601129 TATGTTGGCATAAT
1 TATGTTGGCATAAT
*
29601143 TATGTTGGCTTAAT
1 TATGTTGGCATAAT
29601157 TA
1 TA
29601159 GTCTTCCTAA
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:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (14 bp):
TATGTTGGCATAAT
Found at i:29604911 original size:21 final size:21
Alignment explanation
Indices: 29604887--29604951 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
29604877 GATAGTTCTA
29604887 TTTTACCAGGCAATTGGCTTT
1 TTTTACCAGGCAATTGGCTTT
** * *
29604908 TTTTATCC-GTTAGTT--C-TA
1 TTTTA-CCAGGCAATTGGCTTT
29604926 TTTTACCAGGCAATTGGCTTT
1 TTTTACCAGGCAATTGGCTTT
29604947 TTTTA
1 TTTTA
29604952 TCCTGGTTCT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
17 2 0.06
18 10 0.32
19 1 0.03
20 1 0.03
21 15 0.48
22 2 0.06
ACGTcount: A:0.18, C:0.17, G:0.15, T:0.49
Consensus pattern (21 bp):
TTTTACCAGGCAATTGGCTTT
Found at i:29604933 original size:39 final size:39
Alignment explanation
Indices: 29604879--29604954 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
29604869 GCCAATAAGA
29604879 TAGTTCTATTTTACCAGGCAATTGGCTTTTTTTATCCGT
1 TAGTTCTATTTTACCAGGCAATTGGCTTTTTTTATCCGT
29604918 TAGTTCTATTTTACCAGGCAATTGGCTTTTTTTATCC
1 TAGTTCTATTTTACCAGGCAATTGGCTTTTTTTATCC
29604955 TGGTTCTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.49
Consensus pattern (39 bp):
TAGTTCTATTTTACCAGGCAATTGGCTTTTTTTATCCGT
Found at i:29604961 original size:37 final size:38
Alignment explanation
Indices: 29604879--29604969 Score: 148
Period size: 39 Copynumber: 2.4 Consensus size: 38
29604869 GCCAATAAGA
29604879 TAGTTCTATTTTACCAGGCAATTGGCTTTTTTTATCCG
1 TAGTTCTATTTTACCAGGCAATTGGCTTTTTTTATCCG
29604917 TTAGTTCTATTTTACCAGGCAATTGGCTTTTTTTATCC-
1 -TAGTTCTATTTTACCAGGCAATTGGCTTTTTTTATCCG
*
29604955 TGGTTCTATTATTAC
1 TAGTTCTATT-TTAC
29604970 TGACTTAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
37 9 0.18
38 4 0.08
39 37 0.74
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (38 bp):
TAGTTCTATTTTACCAGGCAATTGGCTTTTTTTATCCG
Found at i:29608826 original size:21 final size:20
Alignment explanation
Indices: 29608789--29608842 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
29608779 CGTAGCCTTG
*
29608789 TGTTGAGCCACAACAACCCTA
1 TGTTGAGCCATAACAA-CCTA
* *
29608810 TGTTGAGCCATATCAACCTG
1 TGTTGAGCCATAACAACCTA
*
29608830 TGTTTAGCCATAA
1 TGTTGAGCCATAA
29608843 AGCCTGCATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (20 bp):
TGTTGAGCCATAACAACCTA
Found at i:29608838 original size:20 final size:21
Alignment explanation
Indices: 29608787--29608842 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
29608777 CACGTAGCCT
*
29608787 TGTGTTGAGCCACAACAACCC
1 TGTGTTGAGCCATAACAACCC
* *
29608808 TATGTTGAGCCATATCAA-CC
1 TGTGTTGAGCCATAACAACCC
*
29608828 TGTGTTTAGCCATAA
1 TGTGTTGAGCCATAA
29608843 AGCCTGCATG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTGTTGAGCCATAACAACCC
Found at i:29612769 original size:37 final size:37
Alignment explanation
Indices: 29612719--29612790 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
29612709 TTTGGCGTCT
*
29612719 GAGCATTTGGCGTGTTATCGGTTGGATTAGCTCTTTG
1 GAGCACTTGGCGTGTTATCGGTTGGATTAGCTCTTTG
*
29612756 GAGCACTTGGCGTGTTTTCGGTTGGATTAGCTCTT
1 GAGCACTTGGCGTGTTATCGGTTGGATTAGCTCTT
29612791 ACGAGCGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.12, C:0.15, G:0.32, T:0.40
Consensus pattern (37 bp):
GAGCACTTGGCGTGTTATCGGTTGGATTAGCTCTTTG
Found at i:29612809 original size:37 final size:37
Alignment explanation
Indices: 29612731--29612809 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
29612721 GCATTTGGCG
* ** * *
29612731 TGTTATCGGTTGGATTAGCTCTTTGGAGCACTTGGCG
1 TGTTTTCGGTTGGATTAGCTCTTACGAGCACTTGACA
**
29612768 TGTTTTCGGTTGGATTAGCTCTTACGAGCGTTTGACA
1 TGTTTTCGGTTGGATTAGCTCTTACGAGCACTTGACA
29612805 TGTTT
1 TGTTT
29612810 CAGGTGGATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.14, C:0.15, G:0.29, T:0.42
Consensus pattern (37 bp):
TGTTTTCGGTTGGATTAGCTCTTACGAGCACTTGACA
Found at i:29613955 original size:20 final size:19
Alignment explanation
Indices: 29613930--29613983 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
29613920 GTGTGTCCCT
29613930 TATTTTTTTGAAAATTTTCA
1 TATTTTTTTG-AAATTTTCA
* *
29613950 TATTTTCTTGAAATTTTCT
1 TATTTTTTTGAAATTTTCA
29613969 TATTTGTTTT-AAATT
1 TATTT-TTTTGAAATT
29613984 AATCTCGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (19 bp):
TATTTTTTTGAAATTTTCA
Found at i:29614370 original size:27 final size:27
Alignment explanation
Indices: 29614334--29614430 Score: 92
Period size: 27 Copynumber: 3.6 Consensus size: 27
29614324 TTCAGATTGC
*
29614334 CACAAGGGCTTCCTTTACATGGATA-A
1 CACAAAGGCTTCCTTTACATGGATAGA
* *
29614360 CATCAAAGGCTTCCTTTACATGTATAGC
1 CA-CAAAGGCTTCCTTTACATGGATAGA
* *
29614388 CACAAAGGC-TCCTATTACA-GAGATTGC
1 CACAAAGGCTTCCT-TTACATG-GATAGA
*
29614415 CACAAAGGCTTTCTTT
1 CACAAAGGCTTCCTTT
29614431 TCAAATATGC
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
26 7 0.12
27 48 0.80
28 5 0.08
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (27 bp):
CACAAAGGCTTCCTTTACATGGATAGA
Found at i:29614526 original size:28 final size:27
Alignment explanation
Indices: 29614386--29614584 Score: 126
Period size: 26 Copynumber: 7.4 Consensus size: 27
29614376 TACATGTATA
* * *
29614386 GCCACAAAGG-CTCCTATTACAGAGATT
1 GCCACAAAGGATTCC-ATTTCAGATATT
* * * *
29614413 GCCACAAAGGCTTTCTTTTCAAATA-T
1 GCCACAAAGGATTCCATTTCAGATATT
* *
29614439 GCCACAAAGGTTTTCATTTC--ATATGT
1 GCCACAAAGGATTCCATTTCAGATAT-T
* *
29614465 GCCACAAAGGCTTCCATTTTATG-TA-T
1 GCCACAAAGGATTCCATTTCA-GATATT
29614491 GCCACAAAGGATTCCATTTCAGATATT
1 GCCACAAAGGATTCCATTTCAGATATT
* **
29614518 CGCCACAAAGGCTTTCC-TTTCAGAGGTCT
1 -GCCACAAAGG-ATTCCATTTCAGATAT-T
**
29614547 GCCACAAAGGCATTCC-TTTCAGAGGTT
1 GCCACAAAGG-ATTCCATTTCAGATATT
29614574 CGCCACAAAGG
1 -GCCACAAAGG
29614585 CTTTCCTTTT
Statistics
Matches: 143, Mismatches: 17, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
24 3 0.02
25 1 0.01
26 59 0.41
27 18 0.13
28 57 0.40
29 5 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (27 bp):
GCCACAAAGGATTCCATTTCAGATATT
Found at i:29614552 original size:56 final size:53
Alignment explanation
Indices: 29614363--29614593 Score: 213
Period size: 56 Copynumber: 4.3 Consensus size: 53
29614353 TGGATAACAT
* * *
29614363 CAAAGGC-TTCCTTTACATGTATAGCCACAAAGG-CTCCTATTACAGAGATTGCCA
1 CAAAGGCTTTCCTTT-CAAGTAT-GCCACAAAGGATTCC-ATTTCAGAGATTGCCA
* * * * *
29614417 CAAAGGCTTTCTTTTCAAATATGCCACAAAGGTTTTCATTTC--ATATGTGCCA
1 CAAAGGCTTTCCTTTCAAGTATGCCACAAAGGATTCCATTTCAGAGAT-TGCCA
* * *
29614469 CAAAGGC-TTCCATTTTATGTATGCCACAAAGGATTCCATTTCAGATATTCGCCA
1 CAAAGGCTTTCC-TTTCAAGTATGCCACAAAGGATTCCATTTCAGAGATT-GCCA
* *
29614523 CAAAGGCTTTCCTTTCAGAGGTCTGCCACAAAGGCATTCC-TTTCAGAGGTTCGCCA
1 CAAAGGCTTTCCTTTCA-A-GTATGCCACAAAGG-ATTCCATTTCAGAGATT-GCCA
29614579 CAAAGGCTTTCCTTT
1 CAAAGGCTTTCCTTT
29614594 TCTGGTGTTT
Statistics
Matches: 148, Mismatches: 18, Indels: 20
0.80 0.10 0.11
Matches are distributed among these distances:
51 6 0.04
52 37 0.25
53 15 0.10
54 33 0.22
55 10 0.07
56 42 0.28
57 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (53 bp):
CAAAGGCTTTCCTTTCAAGTATGCCACAAAGGATTCCATTTCAGAGATTGCCA
Found at i:29614585 original size:28 final size:28
Alignment explanation
Indices: 29614491--29614593 Score: 138
Period size: 28 Copynumber: 3.7 Consensus size: 28
29614481 TTTTATGTAT
**
29614491 GCCACAAAGG-ATTCCATTTCAGATATTC
1 GCCACAAAGGCATTCC-TTTCAGAGGTTC
*
29614519 GCCACAAAGGCTTTCCTTTCAGAGG-TC
1 GCCACAAAGGCATTCCTTTCAGAGGTTC
29614546 TGCCACAAAGGCATTCCTTTCAGAGGTTC
1 -GCCACAAAGGCATTCCTTTCAGAGGTTC
*
29614575 GCCACAAAGGCTTTCCTTT
1 GCCACAAAGGCATTCCTTT
29614594 TCTGGTGTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
27 2 0.03
28 59 0.88
29 6 0.09
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (28 bp):
GCCACAAAGGCATTCCTTTCAGAGGTTC
Found at i:29617101 original size:17 final size:17
Alignment explanation
Indices: 29617079--29617112 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29617069 TATCAGTTGC
*
29617079 TATTTCAATAGCATTTT
1 TATTTCAATAACATTTT
29617096 TATTTCAATAACATTTT
1 TATTTCAATAACATTTT
29617113 CCATTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTCAATAACATTTT
Found at i:29617120 original size:18 final size:17
Alignment explanation
Indices: 29617080--29617121 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
29617070 ATCAGTTGCT
* *
29617080 ATTTCAATAGCATTTTT
1 ATTTCAATAACATTTTC
29617097 ATTTCAATAACATTTTCC
1 ATTTCAATAACATTTT-C
29617115 ATTTCAA
1 ATTTCAA
29617122 AATCAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTTCAATAACATTTTC
Found at i:29618454 original size:35 final size:34
Alignment explanation
Indices: 29618414--29618627 Score: 115
Period size: 35 Copynumber: 5.9 Consensus size: 34
29618404 AAATGCGACG
*
29618414 TTAAAAGGTTGGGATAGACAGGTTCTAAGGCAACC
1 TTAAAAGGTTGGGATAGACATG-TCTAAGGCAACC
* * * *
29618449 TTAAAAGGGTTGAGATAGACTCATCTAAGTCTATGCCGACC
1 TTAAAA-GGTTGGGATAGA--CA--T--GTCTAAGGCAACC
* * * * * *
29618490 TTTAAAGAGTT-GGATCATGCCCATGTCAAATGCGACGT
1 TTAAAAG-GTTGGGAT-A-G-ACATGTCTAAGGCAAC-C
* *
29618528 TTAAAAGGTTGGGATAGATAGGTTCTAAGGCAACC
1 TTAAAAGGTTGGGATAGACATG-TCTAAGGCAACC
* * *
29618563 TTAAAAGGGTTAGAATAGACCTGTCTAAGGCAACC
1 TTAAAA-GGTTGGGATAGACATGTCTAAGGCAACC
* *
29618598 TTCAAAAGGTTAGGATAGACACGTCTAAGG
1 TT-AAAAGGTTGGGATAGACATGTCTAAGG
29618628 TAATTTTTTT
Statistics
Matches: 134, Mismatches: 29, Indels: 32
0.69 0.15 0.16
Matches are distributed among these distances:
35 48 0.36
36 35 0.26
37 12 0.09
38 12 0.09
39 1 0.01
40 4 0.03
41 20 0.15
42 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (34 bp):
TTAAAAGGTTGGGATAGACATGTCTAAGGCAACC
Found at i:29618591 original size:114 final size:113
Alignment explanation
Indices: 29618367--29618582 Score: 362
Period size: 114 Copynumber: 1.9 Consensus size: 113
29618357 AAAGCATACA
* *
29618367 TATGCCGACCTTTAAAGAGTTGGGTCATGCCTACATCAAATGCGACGTTAAAAGGTTGGGATAGA
1 TATGCCGACCTTTAAAGAGTTGGATCATGCCCACATCAAATGCGACGTTAAAAGGTTGGGATAGA
29618432 CAGGTTCTAAGGCAACCTTAAAAGGGTTGAGATAGACTCATCTAAGTC
66 CAGGTTCTAAGGCAACCTTAAAAGGGTTGAGATAGACTCATCTAAGTC
**
29618480 TATGCCGACCTTTAAAGAGTTGGATCATGCCCATGTCAAATGCGACGTTTAAAAGGTTGGGATAG
1 TATGCCGACCTTTAAAGAGTTGGATCATGCCCACATCAAATGCGACG-TTAAAAGGTTGGGATAG
*
29618545 ATAGGTTCTAAGGCAACCTTAAAAGGGTT-AGAATAGAC
65 ACAGGTTCTAAGGCAACCTTAAAAGGGTTGAG-ATAGAC
29618583 CTGTCTAAGG
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
113 45 0.47
114 51 0.53
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (113 bp):
TATGCCGACCTTTAAAGAGTTGGATCATGCCCACATCAAATGCGACGTTAAAAGGTTGGGATAGA
CAGGTTCTAAGGCAACCTTAAAAGGGTTGAGATAGACTCATCTAAGTC
Found at i:29619477 original size:39 final size:39
Alignment explanation
Indices: 29619428--29619505 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
29619418 ACCAAACTTG
* *
29619428 AATATTCTAACAACTTACGACTACTAAATCCAAAGATAA
1 AATATACTAACAACTTACAACTACTAAATCCAAAGATAA
29619467 AATATACTAACAACTTACAACTACTAAATCCAAAGATAA
1 AATATACTAACAACTTACAACTACTAAATCCAAAGATAA
29619506 CTATTCTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.24
Consensus pattern (39 bp):
AATATACTAACAACTTACAACTACTAAATCCAAAGATAA
Found at i:29621815 original size:14 final size:14
Alignment explanation
Indices: 29621798--29621833 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
29621788 TATAACATAT
29621798 ATATTAATGTTAAC
1 ATATTAATGTTAAC
29621812 ATATTAATGTTAAC
1 ATATTAATGTTAAC
*
29621826 ATAATAAT
1 ATATTAAT
29621834 ATATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (14 bp):
ATATTAATGTTAAC
Found at i:29625171 original size:12 final size:12
Alignment explanation
Indices: 29625154--29625178 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29625144 GTCCGTGTTG
29625154 AACTTAAATTTT
1 AACTTAAATTTT
29625166 AACTTAAATTTT
1 AACTTAAATTTT
29625178 A
1 A
29625179 GTTACAACAG
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
AACTTAAATTTT
Found at i:29627549 original size:20 final size:20
Alignment explanation
Indices: 29627524--29627564 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
29627514 ATGACCTACA
29627524 AAAAAAATGAAAAAACAACT
1 AAAAAAATGAAAAAACAACT
*
29627544 AAAAAAATGGAAAAACAACT
1 AAAAAAATGAAAAAACAACT
29627564 A
1 A
29627565 TGTAAGCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAAAATGAAAAAACAACT
Found at i:29629903 original size:18 final size:18
Alignment explanation
Indices: 29629863--29629903 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
29629853 TTAATCTTTG
29629863 ATTTA-TTATTTTATTTT
1 ATTTATTTATTTTATTTT
*
29629880 AGTTATTTATTTTAATTTT
1 ATTTATTTATTTT-ATTTT
29629899 -TTTAT
1 ATTTAT
29629904 CTGACTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTATTTATTTTATTTT
Found at i:29633027 original size:28 final size:28
Alignment explanation
Indices: 29632981--29633037 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
29632971 TATAGTTTTT
29632981 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
29633009 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
29633037 A
1 A
29633038 AAAAACAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:29634022 original size:21 final size:22
Alignment explanation
Indices: 29633996--29634038 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29633986 GAGTTGAAAT
29633996 TAAAGTTATGAAT-TAT-ATATA
1 TAAAGTT-TGAATGTATGATATA
29634017 TAAAGTTTGAATGTATGATATA
1 TAAAGTTTGAATGTATGATATA
29634039 AGTTCTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (22 bp):
TAAAGTTTGAATGTATGATATA
Done.