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 9 of 208
Found at i:2950938 original size:20 final size:21
Alignment explanation
Indices: 2950913--2950956 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
2950903 GTAAGTCATT
2950913 TAATCAATAATCAATAAT-AA
1 TAATCAATAATCAATAATCAA
2950933 TAATCAATAATCAATAATCAA
1 TAATCAATAATCAATAATCAA
2950954 TAA
1 TAA
2950957 GATAGTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (21 bp):
TAATCAATAATCAATAATCAA
Found at i:2960399 original size:13 final size:13
Alignment explanation
Indices: 2960381--2960406 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2960371 TTGCAGACTA
2960381 AGTGTGAAAGTCT
1 AGTGTGAAAGTCT
2960394 AGTGTGAAAGTCT
1 AGTGTGAAAGTCT
2960407 CGATCCGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
AGTGTGAAAGTCT
Found at i:2973440 original size:26 final size:26
Alignment explanation
Indices: 2973402--2973456 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
2973392 CAAACATATC
* *
2973402 CCATAGATGCCACTTGATATCAAACA
1 CCATAGATACCACTCGATATCAAACA
*
2973428 CCATAGATACCACTCGATATCAAGCA
1 CCATAGATACCACTCGATATCAAACA
2973454 CCA
1 CCA
2973457 CCATGAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.31, G:0.11, T:0.20
Consensus pattern (26 bp):
CCATAGATACCACTCGATATCAAACA
Found at i:2979820 original size:13 final size:13
Alignment explanation
Indices: 2979802--2979835 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2979792 TAGGTGCCTG
2979802 AAAAAAATAAAAT
1 AAAAAAATAAAAT
*
2979815 AAAAAAATAACAT
1 AAAAAAATAAAAT
*
2979828 AATAAAAT
1 AAAAAAAT
2979836 GTTTGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:2982090 original size:20 final size:20
Alignment explanation
Indices: 2982065--2982105 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2982055 TTAAGTTCTC
*
2982065 TATTTT-TTTGTTTTTTTATT
1 TATTTTATTT-TTCTTTTATT
2982085 TATTTTATTTTTCTTTTATT
1 TATTTTATTTTTCTTTTATT
2982105 T
1 T
2982106 TTTCTCTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (20 bp):
TATTTTATTTTTCTTTTATT
Found at i:2982736 original size:2 final size:2
Alignment explanation
Indices: 2982729--2982779 Score: 86
Period size: 2 Copynumber: 25.5 Consensus size: 2
2982719 AACTTTGTTT
2982729 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
2982771 TA TA TA TA T
1 TA TA TA TA T
2982780 TTTTATATTC
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 45 0.96
3 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2989826 original size:13 final size:13
Alignment explanation
Indices: 2989808--2989832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2989798 TTATCATCTA
2989808 TCATTTATTTATT
1 TCATTTATTTATT
2989821 TCATTTATTTAT
1 TCATTTATTTAT
2989833 CTACGCATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TCATTTATTTATT
Found at i:2990558 original size:22 final size:22
Alignment explanation
Indices: 2990531--2990599 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
2990521 CCCTTGATCC
2990531 TTTTAACACTAT-TTTTATATAT
1 TTTTAA-ACTATCTTTTATATAT
*
2990553 TTTTAAACTGTCTTTT-T-TAT
1 TTTTAAACTATCTTTTATATAT
*
2990573 TATTTAAGACTTTCTTTTATATAT
1 T-TTTAA-ACTATCTTTTATATAT
2990597 TTT
1 TTT
2990600 ATTTTAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 4 0.10
21 10 0.25
22 19 0.47
23 3 0.08
24 4 0.10
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (22 bp):
TTTTAAACTATCTTTTATATAT
Found at i:2990972 original size:38 final size:37
Alignment explanation
Indices: 2990888--2990982 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
2990878 TATACGTACT
*
2990888 TATACATACTTAAATATATTTTTCATATTTCATAATTC
1 TATACATACTTAAATATATTTTACATATTT-ATAATTC
* *
2990926 T-TATATACTTACATATATTTATACATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TACATATTTATA-ATTC
*
2990962 ATATACATACTTATATATATT
1 -TATACATACTTAAATATATT
2990983 CTTTATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.08
37 19 0.40
38 25 0.52
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTACATATTTATAATTC
Found at i:2991640 original size:106 final size:106
Alignment explanation
Indices: 2991452--2991652 Score: 393
Period size: 106 Copynumber: 1.9 Consensus size: 106
2991442 AAAGTTTTTC
2991452 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
2991517 TTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTT
66 TTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTT
2991558 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
2991623 TTCTCGTTCGACTAAATAGCCAAATATCCT
66 TTCTCGTTCGACCAAATAGCCAAATATCCT
2991653 CTTAAAGCTT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 94 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (106 bp):
TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTT
Found at i:2997763 original size:20 final size:20
Alignment explanation
Indices: 2997738--2997779 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2997728 CTTTAAATAA
2997738 TTAAATAAAATTTTTATCAT
1 TTAAATAAAATTTTTATCAT
*
2997758 TTAAATAAATTTTTTATCAT
1 TTAAATAAAATTTTTATCAT
2997778 TT
1 TT
2997780 TTGAGATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAATAAAATTTTTATCAT
Found at i:3006769 original size:13 final size:13
Alignment explanation
Indices: 3006751--3006775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3006741 AATAAATATG
3006751 TTAATTCATTTAA
1 TTAATTCATTTAA
3006764 TTAATTCATTTA
1 TTAATTCATTTA
3006776 TATTTTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTCATTTAA
Found at i:3023195 original size:3 final size:3
Alignment explanation
Indices: 3023187--3023222 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3023177 GCCTTACTAT
3023187 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3023223 GACAAGCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3023623 original size:44 final size:44
Alignment explanation
Indices: 3023560--3023654 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
3023550 TGCCCTTAAA
*
3023560 CATTTCATGCATTCATCATCTAAACATATCACAATCATCCAAGC
1 CATTTCATGCATTCATCATCTAAACATATCACAATCACCCAAGC
*
3023604 CATTTCTTGCATTCATCATCTAAACATATCACAATCACCCAAGC
1 CATTTCATGCATTCATCATCTAAACATATCACAATCACCCAAGC
*
3023648 CAATTCA
1 CATTTCA
3023655 ACTTTCACAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (44 bp):
CATTTCATGCATTCATCATCTAAACATATCACAATCACCCAAGC
Found at i:3027347 original size:32 final size:32
Alignment explanation
Indices: 3027264--3027347 Score: 118
Period size: 32 Copynumber: 2.6 Consensus size: 32
3027254 ATATGTTTTG
3027264 TATATTGCCGAATTGA-TT-TATATGTATATA
1 TATATTGCCGAATTGATTTGTATATGTATATA
* *
3027294 TATACATTGTCGAATTGATTTGTCTATGTATATA
1 TAT--ATTGCCGAATTGATTTGTATATGTATATA
3027328 TATATTGCCGAATTGATTTG
1 TATATTGCCGAATTGATTTG
3027348 AGCATTGGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.06
32 28 0.60
33 2 0.04
34 14 0.30
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.46
Consensus pattern (32 bp):
TATATTGCCGAATTGATTTGTATATGTATATA
Found at i:3027567 original size:48 final size:48
Alignment explanation
Indices: 3027515--3027687 Score: 240
Period size: 48 Copynumber: 3.6 Consensus size: 48
3027505 TGAGAAAATC
*
3027515 TATAAGACCATATCTGGGATATGGCATCGGCATTGATTTAAGATCCCG
1 TATAAGACCATATCTGGGATATGGCATCGGCATTGATTTGAGATCCCG
* * * * *
3027563 TATAAGACCATATCTGGGATATGACATCGACATCGATTCGAGATCCCA
1 TATAAGACCATATCTGGGATATGGCATCGGCATTGATTTGAGATCCCG
* **
3027611 TATAAGACCATATCTGGGAGATGGCA-CTGGCATTGATTTGAGATTTCG
1 TATAAGACCATATCTGGGATATGGCATC-GGCATTGATTTGAGATCCCG
*
3027659 TATAAGACCATATCTGGGATATAGCATCG
1 TATAAGACCATATCTGGGATATGGCATCG
3027688 TTATGAGACT
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.01
48 105 0.98
49 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (48 bp):
TATAAGACCATATCTGGGATATGGCATCGGCATTGATTTGAGATCCCG
Found at i:3027770 original size:43 final size:42
Alignment explanation
Indices: 3027638--3027771 Score: 144
Period size: 42 Copynumber: 3.1 Consensus size: 42
3027628 GAGATGGCAC
* * * *
3027638 TGGCATTGATTTGAGATTTCGTATAAGACCATATCTGGGATA
1 TGGCATCGATATGAGATTTCGTGTAAGACCATGTCTGGGATA
* * * *
3027680 TAGCATCGTTATGAGACTTCGTGTAATACCATAG-CTGGGATA
1 TGGCATCGATATGAGATTTCGTGTAAGACCAT-GTCTGGGATA
* *
3027722 TTGGCATCGATATGAGATTTCCATGTAAGACCATGTCTGGGACA
1 -TGGCATCGATATGAGATTT-CGTGTAAGACCATGTCTGGGATA
3027766 TGGCAT
1 TGGCAT
3027772 TTGTACGATA
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
42 33 0.45
43 23 0.31
44 18 0.24
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (42 bp):
TGGCATCGATATGAGATTTCGTGTAAGACCATGTCTGGGATA
Found at i:3028695 original size:57 final size:57
Alignment explanation
Indices: 3028626--3028740 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
3028616 GTCTAGTTTT
** *
3028626 GGTAAAATCAAGTGGATCTTAATTTGGAGTTCTGTAGCGCAAGATATAAATAATTTA
1 GGTAAAATCAAGTGGATCTTAATTTAAAGTTCTGTAGCACAAGATATAAATAATTTA
3028683 GGTAAAATCAAGTGGATCTTAATTTAAAGTTCTGTAGCACAAGATATAAATAATTTA
1 GGTAAAATCAAGTGGATCTTAATTTAAAGTTCTGTAGCACAAGATATAAATAATTTA
3028740 G
1 G
3028741 TGACTATCAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (57 bp):
GGTAAAATCAAGTGGATCTTAATTTAAAGTTCTGTAGCACAAGATATAAATAATTTA
Found at i:3038035 original size:15 final size:15
Alignment explanation
Indices: 3038010--3038044 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3038000 AACTCTATTT
*
3038010 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
3038024 TAATTAATATTAAGA
1 TAATTAATATTAAGA
3038039 TAATTA
1 TAATTA
3038045 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:3047410 original size:42 final size:42
Alignment explanation
Indices: 3047358--3047445 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
3047348 AAAGCCCAAA
* * *
3047358 GGTTGCACGAAAGAACATAAGTGCTAAACT-GAAACCTATAAG
1 GGTTGAACGAAAGAACATAAGAGCTAAA-TGGAAACCCATAAG
** *
3047400 GGTTGAACGAAAGCTCATAAGAGCTAAATGGAAACCCATGAG
1 GGTTGAACGAAAGAACATAAGAGCTAAATGGAAACCCATAAG
3047442 GGTT
1 GGTT
3047446 AAACTGAAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19
Consensus pattern (42 bp):
GGTTGAACGAAAGAACATAAGAGCTAAATGGAAACCCATAAG
Found at i:3047456 original size:42 final size:41
Alignment explanation
Indices: 3047373--3047532 Score: 137
Period size: 42 Copynumber: 3.8 Consensus size: 41
3047363 CACGAAAGAA
* * *
3047373 CATAAGTGCTAAACTGAAACCTATAAGGGTTGAAC-GAAAGCT
1 CATAAGAGCTAAA-TGAAACCCATAAGGGTTAAACTG-AAGCT
*
3047415 CATAAGAGCTAAATGGAAACCCATGAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAAT-GAAACCCATAAGGGTTAAACTGAAGCT
* * * * * * *
3047457 CAAAAGAGCTGAACTAAAACTCAAAAGGGTTATACTAAAGCT
1 CATAAGAGCT-AAATGAAACCCATAAGGGTTAAACTGAAGCT
*
3047499 CA-AAGAGCTAAACGGAAACCCATTAA-GGTTAAAC
1 CATAAGAGCTAAA-TGAAACCCA-TAAGGGTTAAAC
3047533 GGTAACTTGT
Statistics
Matches: 95, Mismatches: 18, Indels: 11
0.77 0.15 0.09
Matches are distributed among these distances:
40 2 0.02
41 21 0.22
42 68 0.72
43 4 0.04
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (41 bp):
CATAAGAGCTAAATGAAACCCATAAGGGTTAAACTGAAGCT
Found at i:3049306 original size:188 final size:189
Alignment explanation
Indices: 3048988--3049360 Score: 685
Period size: 188 Copynumber: 2.0 Consensus size: 189
3048978 GTGGGGAACA
3048988 AAGCTTTTAGATGGATGGTTGGGAATGGAAGGATGGCGATGTTTTGAGAGGATATTTGGTGTTGT
1 AAGCTTTTAGATGGATGGTTGGGAATGGAAGGATGGCGATGTTTTGAGAGGATATTTGGTGTTGT
* *
3049053 AATCAACCACAAAAAAAAAAGAATTTCCTAGAGTTTTTCGCTTAGCAAGAAAAAAGAAAGGTATG
66 AATCAACCACAAAAAAAAAAGAATTTCCTAGAGTGTTCCGCTTAGCAAGAAAAAAGAAAGGTATG
3049118 GTAACAGATTACTCGAGCAACAATGGTTTCAGCAATATGAATTACGGTGAATTCTAACG
131 GTAACAGATTACTCGAGCAACAATGGTTTCAGCAATATGAATTACGGTGAATTCTAACG
3049177 AAGCTTTTAGATGGATGGTTGGGAATGGAAGGAT-GCGATGTTTTGAGAGGATATTTGGTGTTGT
1 AAGCTTTTAGATGGATGGTTGGGAATGGAAGGATGGCGATGTTTTGAGAGGATATTTGGTGTTGT
3049241 AATCAACCACAAAAAAAAAAGAATTTCCTAGAGTGTTCCGCTTAGCAAGAAAAAAGAAAGGTATG
66 AATCAACCACAAAAAAAAAAGAATTTCCTAGAGTGTTCCGCTTAGCAAGAAAAAAGAAAGGTATG
* * * *
3049306 GTAACAGATTACTCGAGCAACAATGGTTTTAGCAATGTGAATTATGGTTAATTCT
131 GTAACAGATTACTCGAGCAACAATGGTTTCAGCAATATGAATTACGGTGAATTCT
3049361 TTACACGAAC
Statistics
Matches: 178, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
188 144 0.81
189 34 0.19
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.29
Consensus pattern (189 bp):
AAGCTTTTAGATGGATGGTTGGGAATGGAAGGATGGCGATGTTTTGAGAGGATATTTGGTGTTGT
AATCAACCACAAAAAAAAAAGAATTTCCTAGAGTGTTCCGCTTAGCAAGAAAAAAGAAAGGTATG
GTAACAGATTACTCGAGCAACAATGGTTTCAGCAATATGAATTACGGTGAATTCTAACG
Found at i:3050711 original size:3 final size:3
Alignment explanation
Indices: 3050703--3050753 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3050693 GCCTTACTAT
3050703 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3050751 ATA
1 ATA
3050754 GACAAGCTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3052383 original size:20 final size:20
Alignment explanation
Indices: 3052360--3052400 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3052350 ACACGGGCGT
*
3052360 GTAGACCACCACACGACCTA
1 GTAGACCACCACACAACCTA
*
3052380 GTAGACCTCCACACAACCTA
1 GTAGACCACCACACAACCTA
3052400 G
1 G
3052401 GCACTACCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.39, G:0.15, T:0.12
Consensus pattern (20 bp):
GTAGACCACCACACAACCTA
Found at i:3053628 original size:46 final size:46
Alignment explanation
Indices: 3053561--3053655 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
3053551 CAGAACTGTC
3053561 AAATGATTCCATAAGAATTACTTCCGACTTGCGTCGAATGCCATTT
1 AAATGATTCCATAAGAATTACTTCCGACTTGCGTCGAATGCCATTT
*
3053607 AAATGATTCCATATGAATTACTTCCGACTTGCGTCGAATGCCATTT
1 AAATGATTCCATAAGAATTACTTCCGACTTGCGTCGAATGCCATTT
3053653 AAA
1 AAA
3053656 CTTTGTTTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.33
Consensus pattern (46 bp):
AAATGATTCCATAAGAATTACTTCCGACTTGCGTCGAATGCCATTT
Found at i:3054031 original size:22 final size:23
Alignment explanation
Indices: 3053995--3054044 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
3053985 AAATATAACC
*
3053995 GATTTTGAAATAAAATTTAAACA
1 GATTCTGAAATAAAATTTAAACA
*
3054018 GATTCTGAAA-AAAATTTTAACA
1 GATTCTGAAATAAAATTTAAACA
3054040 GATTC
1 GATTC
3054045 CCTAAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (23 bp):
GATTCTGAAATAAAATTTAAACA
Found at i:3054051 original size:22 final size:22
Alignment explanation
Indices: 3054006--3054052 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3053996 ATTTTGAAAT
**
3054006 AAAATTTAAACAGATTCTGAAA
1 AAAATTTAAACAGATTCCCAAA
* *
3054028 AAAATTTTAACAGATTCCCTAA
1 AAAATTTAAACAGATTCCCAAA
3054050 AAA
1 AAA
3054053 TCGTGGTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (22 bp):
AAAATTTAAACAGATTCCCAAA
Found at i:3060957 original size:20 final size:19
Alignment explanation
Indices: 3060906--3060962 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
3060896 CATTTTTATT
* *
3060906 TAATAAATTAGAATTCATA
1 TAATAAATTATAATTAATA
**
3060925 TAAGCAA-TATAATTAATCA
1 TAATAAATTATAATTAAT-A
3060944 TAATAAATTATAATTAATA
1 TAATAAATTATAATTAATA
3060963 GGCTTGTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
18 8 0.27
19 12 0.40
20 10 0.33
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (19 bp):
TAATAAATTATAATTAATA
Found at i:3061724 original size:38 final size:39
Alignment explanation
Indices: 3061673--3061748 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 39
3061663 AGGGTTTAAT
* * **
3061673 TAATTATTTAAATAAAAATTATTAAAATTTTAAAAAATC
1 TAATTATTAAAATAAAAATTATAAAAATCATAAAAAATC
*
3061712 TAATT-TTAAAATATAAATTATAAAAATCATAAAAAAT
1 TAATTATTAAAATAAAAATTATAAAAATCATAAAAAAT
3061749 ATTTTAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 27 0.84
39 5 0.16
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (39 bp):
TAATTATTAAAATAAAAATTATAAAAATCATAAAAAATC
Found at i:3062649 original size:20 final size:21
Alignment explanation
Indices: 3062613--3062655 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3062603 TTAATGTCTT
3062613 ATAATTGTTTATAAATTTATA
1 ATAATTGTTTATAAATTTATA
* *
3062634 ATAATT-TTTATGAATTTTTA
1 ATAATTGTTTATAAATTTATA
3062654 AT
1 AT
3062656 TTATATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATAATTGTTTATAAATTTATA
Found at i:3077979 original size:25 final size:26
Alignment explanation
Indices: 3077926--3077979 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
3077916 TTTATATCGT
*
3077926 GAATTACTATCAAATAAAGAAAGTGA
1 GAATTACTATCAAAAAAAGAAAGTGA
*
3077952 GAATTA-TATTAAAAAAAGGAAAGT-A
1 GAATTACTATCAAAAAAA-GAAAGTGA
3077977 GAA
1 GAA
3077980 ATCAAATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.57, C:0.04, G:0.17, T:0.22
Consensus pattern (26 bp):
GAATTACTATCAAAAAAAGAAAGTGA
Found at i:3079558 original size:98 final size:96
Alignment explanation
Indices: 3079372--3079563 Score: 240
Period size: 97 Copynumber: 2.0 Consensus size: 96
3079362 CAAACGCCGG
* ** * * *
3079372 TAATGTATAGTATTAGCGGCGCTTAGCGGAAGCGCCGCAAAAGATGTTAACCAAAACGCAGAGTT
1 TAATGTATAGTATTAGCGGCACCGAGCGGAAACGCCGCAAAACATCTTAACCAAAACGCAGAGTT
* * *
3079437 TGGTCTTGATGTATATTGCAATTAGTGGCGC
66 TGGTATTGATGTATACTACAATTAGTGGCGC
* * * *
3079468 TAATGTATAGTATTAGCGGCACCGAGCGTTAAACGCCGCAAGACATCTTAATCAAAACGCAGCGT
1 TAATGTATAGTATTAGCGGCACCGAGCG-GAAACGCCGCAAAACATCTTAACCAAAACGCAGAG-
*
3079533 TTTGGTATTGATGTATACTATAATTAGTGGC
64 TTTGGTATTGATGTATACTACAATTAGTGGC
3079564 TTTTAAGGAA
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
96 25 0.31
97 28 0.35
98 27 0.34
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (96 bp):
TAATGTATAGTATTAGCGGCACCGAGCGGAAACGCCGCAAAACATCTTAACCAAAACGCAGAGTT
TGGTATTGATGTATACTACAATTAGTGGCGC
Found at i:3079956 original size:18 final size:18
Alignment explanation
Indices: 3079935--3079970 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3079925 TCATTTTATA
3079935 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
3079953 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
3079971 AAAATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:3080936 original size:7 final size:7
Alignment explanation
Indices: 3080911--3080973 Score: 81
Period size: 7 Copynumber: 8.9 Consensus size: 7
3080901 GACTTTTACT
3080911 GTTTGGG
1 GTTTGGG
*
3080918 GCTTTAGG
1 G-TTTGGG
3080926 GTTTGGG
1 GTTTGGG
*
3080933 GTTTGAG
1 GTTTGGG
3080940 GTTTGGG
1 GTTTGGG
**
3080947 GTTTTTG
1 GTTTGGG
3080954 GTTTGGG
1 GTTTGGG
3080961 GTTTGGG
1 GTTTGGG
3080968 GTTTGG
1 GTTTGG
3080974 TTTTTGAGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
7 41 0.87
8 6 0.13
ACGTcount: A:0.03, C:0.02, G:0.49, T:0.46
Consensus pattern (7 bp):
GTTTGGG
Found at i:3080944 original size:14 final size:14
Alignment explanation
Indices: 3080911--3080985 Score: 80
Period size: 14 Copynumber: 5.3 Consensus size: 14
3080901 GACTTTTACT
3080911 GTTTGGGGCTTT-AGG
1 GTTTGGGG-TTTGA-G
3080926 GTTTGGGGTTTGAG
1 GTTTGGGGTTTGAG
**
3080940 GTTTGGGGTTTTTG
1 GTTTGGGGTTTGAG
*
3080954 GTTTGGGGTTTGGG
1 GTTTGGGGTTTGAG
**
3080968 GTTTGGTTTTTGAG
1 GTTTGGGGTTTGAG
3080982 GTTT
1 GTTT
3080986 AAGGTTTAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
14 43 0.83
15 9 0.17
ACGTcount: A:0.04, C:0.01, G:0.45, T:0.49
Consensus pattern (14 bp):
GTTTGGGGTTTGAG
Found at i:3080949 original size:21 final size:21
Alignment explanation
Indices: 3080924--3080985 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
3080914 TGGGGCTTTA
3080924 GGGTTTGGGGTTTGAGGTTTG
1 GGGTTTGGGGTTTGAGGTTTG
** *
3080945 GGGTTTTTGGTTTGGGGTTTG
1 GGGTTTGGGGTTTGAGGTTTG
**
3080966 GGGTTTGGTTTTTGAGGTTT
1 GGGTTTGGGGTTTGAGGTTT
3080986 AAGGTTTAGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (21 bp):
GGGTTTGGGGTTTGAGGTTTG
Found at i:3080960 original size:28 final size:29
Alignment explanation
Indices: 3080911--3080973 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
3080901 GACTTTTACT
3080911 GTTTGGGGCTTTAGGGTTTGGGGTTTGAG
1 GTTTGGGGCTTTAGGGTTTGGGGTTTGAG
** *
3080940 GTTTGGGG-TTTTTGGTTTGGGGTTTGGG
1 GTTTGGGGCTTTAGGGTTTGGGGTTTGAG
3080968 GTTTGG
1 GTTTGG
3080974 TTTTTGAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 23 0.74
29 8 0.26
ACGTcount: A:0.03, C:0.02, G:0.49, T:0.46
Consensus pattern (29 bp):
GTTTGGGGCTTTAGGGTTTGGGGTTTGAG
Found at i:3083628 original size:17 final size:17
Alignment explanation
Indices: 3083606--3083640 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3083596 TACATGACTT
3083606 ACATATTACTTACTAAA
1 ACATATTACTTACTAAA
**
3083623 ACATATTTTTTACTAAA
1 ACATATTACTTACTAAA
3083640 A
1 A
3083641 TTTACTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (17 bp):
ACATATTACTTACTAAA
Found at i:3083658 original size:13 final size:13
Alignment explanation
Indices: 3083642--3083700 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
3083632 TTACTAAAAT
*
3083642 TTACTTTAATATA
1 TTACTTAAATATA
*
3083655 TTACTTGAATATA
1 TTACTTAAATATA
3083668 TTACTTAAATA-A
1 TTACTTAAATATA
*
3083680 TTTACTTAAATACA
1 -TTACTTAAATATA
3083694 TTACTTA
1 TTACTTA
3083701 CTAAAATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
12 1 0.02
13 40 0.95
14 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:3084002 original size:13 final size:12
Alignment explanation
Indices: 3083986--3084031 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
3083976 TTACTAAAAT
*
3083986 TTACTTGAATATA
1 TTACTTAAATA-A
3083999 TTACTTAAATAA
1 TTACTTAAATAA
3084011 TTTACTTAAATACA
1 -TTACTTAAATA-A
3084025 TTACTTA
1 TTACTTA
3084032 CTAAAATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 1 0.03
13 28 0.93
14 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (12 bp):
TTACTTAAATAA
Found at i:3084031 original size:344 final size:330
Alignment explanation
Indices: 3083457--3084152 Score: 1126
Period size: 344 Copynumber: 2.1 Consensus size: 330
3083447 AAAGTTAATA
*
3083457 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTGATAAT
1 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAATAAT
* *
3083522 ATATATATTGTTAAGTAATATTTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTA
66 ATATATATTCTTAAGTAATAATTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTA
*
3083587 AGTATATTCTACATGACTTACATATTACTTACTAAAACATATTTTTTACTAAAATTTACTTTAAT
131 AGTATATTCTACATGACTTACA-ATTACTTACTAAAACATATTTTTTACTAAAATTTACTTGAAT
*
3083652 ATATTACTTGAATATATTACTTAAATAATTTACTTAAATACATTACTTACTAAAATTTTTTTAAA
195 ATATTAC-T---TA-A--A--T-AAT--TTTACTTAAATACATTACTTACTAAAATTTGTTTAAA
*** *
3083717 TTTTAAATACATTACTTGTTTAATATATTACTTACTAAAATTTAAGTATATATTACATTCCTTAC
248 TTTTAAATACATTACTTAAAT-ATATATTACTTACTAAAATTTAAGTATATATTACATTACTTAC
3083782 ATAACTTGTTAAAATATAT
312 ATAACTTGTTAAAATATAT
3083801 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAATAAT
1 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAAT-A-
* *
3083866 ATATATATATTCTTAAGTAATAATTTTTTAAAATTTATATCTTACATTACTTAAATGTATATTTT
64 ATATATATATTCTTAAGTAATAATTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTT
*
3083931 TAAGTATATTTTACATGACTTAC-ATTACTTACTAAAACATATTTTTTACTAAAATTTACTTGAA
129 TAAGTATATTCTACATGACTTACAATTACTTACTAAAACATATTTTTTACTAAAATTTACTTGAA
3083995 TATATTACTTAAATAA-TTTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTTAAATACA
194 TATATTACTTAAATAATTTTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTTAAATACA
3084059 TTACTTAAATATATATTACTTACTAAAATTTAAGTATATATTACATTACTTACATAACTTGTTAA
259 TTACTTAAATATATATTACTTACTAAAATTTAAGTATATATTACATTACTTACATAACTTGTTAA
3084124 AATATAT
324 AATATAT
3084131 TATAATTTCAATATTTATTATA
1 TATAATTTCAATATTTATTATA
3084153 AATAAGATAC
Statistics
Matches: 338, Mismatches: 12, Indels: 18
0.92 0.03 0.05
Matches are distributed among these distances:
330 83 0.25
331 54 0.16
334 2 0.01
335 1 0.00
337 1 0.00
339 1 0.00
340 2 0.01
343 1 0.00
344 109 0.32
345 1 0.00
346 83 0.25
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (330 bp):
TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAATAAT
ATATATATTCTTAAGTAATAATTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTA
AGTATATTCTACATGACTTACAATTACTTACTAAAACATATTTTTTACTAAAATTTACTTGAATA
TATTACTTAAATAATTTTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTTAAATACATT
ACTTAAATATATATTACTTACTAAAATTTAAGTATATATTACATTACTTACATAACTTGTTAAAA
TATAT
Found at i:3084366 original size:38 final size:37
Alignment explanation
Indices: 3084271--3084370 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 37
3084261 TCACACATAC
3084271 ACTTAT-TAAACTTACATAATACATGACTTATATAAA
1 ACTTATATAAACTTACATAATACATGACTTATATAAA
* * * *
3084307 ATTCTCAAATAAACTTACATAATACATTAGTTATATAATA
1 A--CTTATATAAACTTACATAATACATGACTTATATAA-A
3084347 ACTTATATAAACTTACATAATACA
1 ACTTATATAAACTTACATAATACA
3084371 CATTACTTAC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
36 1 0.02
38 24 0.44
39 27 0.50
40 2 0.04
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (37 bp):
ACTTATATAAACTTACATAATACATGACTTATATAAA
Found at i:3084401 original size:9 final size:9
Alignment explanation
Indices: 3084344--3084474 Score: 85
Period size: 9 Copynumber: 15.0 Consensus size: 9
3084334 TAGTTATATA
*
3084344 ATAACTTAT
1 ATAACTTAC
3084353 ATAAACTTAC
1 AT-AACTTAC
*
3084363 ATAA-TACAC
1 ATAACT-TAC
*
3084372 ATTACTTAC
1 ATAACTTAC
* *
3084381 ATAGCATAC
1 ATAACTTAC
3084390 ATAACTTAC
1 ATAACTTAC
3084399 ATAA--TAC
1 ATAACTTAC
* *
3084406 ACAACTTAA
1 ATAACTTAC
*
3084415 ATAGCTTAC
1 ATAACTTAC
*
3084424 TTAA--TAC
1 ATAACTTAC
3084431 ATAACTTAC
1 ATAACTTAC
*
3084440 ATAACTTAG
1 ATAACTTAC
* *
3084449 A-CACGTAC
1 ATAACTTAC
3084457 ATAACTTAC
1 ATAACTTAC
*
3084466 ATAATTTAC
1 ATAACTTAC
3084475 TTAATACATA
Statistics
Matches: 90, Mismatches: 24, Indels: 16
0.69 0.18 0.12
Matches are distributed among these distances:
7 12 0.13
8 6 0.07
9 63 0.70
10 9 0.10
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:3084422 original size:25 final size:25
Alignment explanation
Indices: 3084390--3084447 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
3084380 CATAGCATAC
3084390 ATAACTTACATAATACACAACTTAA
1 ATAACTTACATAATACACAACTTAA
* * * *
3084415 ATAGCTTACTTAATACATAACTTAC
1 ATAACTTACATAATACACAACTTAA
3084440 ATAACTTA
1 ATAACTTA
3084448 GACACGTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (25 bp):
ATAACTTACATAATACACAACTTAA
Found at i:3090073 original size:21 final size:21
Alignment explanation
Indices: 3090003--3090060 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
3089993 CTACAACTTA
*
3090003 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGGG
3090024 AAGCAGAGGCCGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGGG
*
3090045 AAGCAGAGGCTGCAGC
1 AAGCAGAGGCCGCAGC
3090061 CAGACAAGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.22, G:0.47, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGGG
Found at i:3090484 original size:24 final size:24
Alignment explanation
Indices: 3090456--3090502 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3090446 TGTAGTGGAA
*
3090456 GAAAGAAAAAGAAAGAAAGAAAAG
1 GAAAGAAAAAGAAAGAAAAAAAAG
* *
3090480 GAAAGGAGAAGAAAGAAAAAAAA
1 GAAAGAAAAAGAAAGAAAAAAAA
3090503 AAAGGAGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (24 bp):
GAAAGAAAAAGAAAGAAAAAAAAG
Found at i:3090506 original size:22 final size:24
Alignment explanation
Indices: 3090464--3090514 Score: 79
Period size: 22 Copynumber: 2.2 Consensus size: 24
3090454 AAGAAAGAAA
*
3090464 AAGAAAGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAGAAAAGAAAAGGAG
3090488 AAGAAAGAAA-AAAA-AAAAGGAG
1 AAGAAAGAAAGAAAAGAAAAGGAG
3090510 AAGAA
1 AAGAA
3090515 GAGGGAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 12 0.46
23 4 0.15
24 10 0.38
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (24 bp):
AAGAAAGAAAGAAAAGAAAAGGAG
Found at i:3091044 original size:152 final size:150
Alignment explanation
Indices: 3090863--3092063 Score: 1234
Period size: 152 Copynumber: 7.9 Consensus size: 150
3090853 AAATTGTATA
*
3090863 TTTAAAAAACACACT-AAATTA-ATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TTTAAAAAACACAATAAAATTATATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
**
3090926 AAATTAAAAAATATGATTTTTTTAAAGTAATAAAACACGGGAGAAAAATACGAACAAAGGGCCGA
66 AAATTAAAAAATATGATTTTTTTAAAGTAATAAAATTCGGGA-AAAAATACGAACAAAGGGCCGA
* * *
3090991 AGTAGGGGTTTTTTACTAAAT
130 AATAAGGGTTTTTTATTAAAT
* * * *
3091012 TTTAAAAAAATAAAAAAAAAATTA-ATACATTTCAAACATAATGTACTAAAATAATGTAAAA-AA
1 TTT-AAAAAA-CACAATAAAATTATATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
* *
3091075 TAAAA-TACAAAAATAAT-ATATTTTATTAAAAGT-A-AAAA-TAGGGAAAAAAAATACGAGCAA
64 TAAAATTA-AAAAAT-ATGAT-TTTT-TT-AAAGTAATAAAATTCGGG--AAAAAATACGAACAA
*
3091135 ATGGCCGAAATAA-GGTTTTTT-TTAAATT
122 AGGGCCGAAATAAGGGTTTTTTATTAAA-T
* * * * *
3091163 TATTTAAAAACACATTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATTTAAAATAAT
1 T-TTAAAAAACACAATAAAATTATATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
* * **
3091228 AAAATTAGAAAATATGATATATTTTAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGGCTA
65 AAAATTAAAAAATATGAT-TTTTTTAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGGCCG
3091293 AAATAAGGGTTTTTTATTAAA-
129 AAATAAGGGTTTTTTATTAAAT
* * * * *
3091314 -TTAAAAAA-AGAA-ATAATTA-ATACATTTCAAGCATAATGTACTAAGATAAAT-TAAAATAAT
1 TTTAAAAAACACAATAAAATTATATAAATTTCAAACATAATGTACTAAAAT-AATGTAAAATAAT
* * *
3091374 AAAATATGAAAATAATAT-ATTTTTATTGAAAGTAATAAAAATCGGGAAAAAATATGAGCAAAGG
65 AAAAT-T-AAAA-AATATGATTTTT-TT-AAAGTAATAAAATTCGGGAAAAAATACGAACAAAGG
*
3091438 GCCGAAATAAGGGTTTTTTAATT-TA-
125 GCCGAAATAAGGGTTTTTT-ATTAAAT
* * * * * *
3091463 TTTAAGAAACACACTAAATTTATTTAAATTTAAAACATAATGTACTAAAATAATATAAAATAATA
1 TTTAAAAAACACAATAAAATTATATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
*
3091528 AAATTATAAAATATAAT-ATTTTTTTAAAGTAATCAAATTCGGGAAAAAAATACGAACAAAGGGC
66 AAATTA-AAAA-AT-ATGATTTTTTTAAAGTAATAAAATTCGGG-AAAAAATACGAACAAAGGGC
* *
3091592 CGAAATAAGGATTTTTTACTAAATTT
127 CGAAATAAGGGTTTTTTATTAAA--T
* * * * * * *
3091618 TTTTAAAAA-AGAAT-TAATTA-ATACATTTAAAACATAATGTACTAAGATAAAGTAAAATAATA
1 TTTAAAAAACACAATAAAATTATATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* * * *
3091680 AAA-TACAAAAATAATATATTTTTATTTAAAGTAATAAAATTCGGGAAAAAGTTCCGAGCAAAGG
66 AAATTA-AAAAAT-AT-GA-TTTT-TTTAAAGTAATAAAATTCGGGAAAAA-ATACGAACAAAGG
* *
3091744 GCCAAAATAACGGTTTTTT-TTAAATTT
125 GCCGAAATAAGGGTTTTTTATTAAA--T
* * *
3091771 ATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
1 -TTTAAAAAACACAATAAAATTATATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
* *
3091836 AAAATTAGAAAATATGATATTTTTTTTAAAGTAATAAAATTCGAGCAAAAAATACGAACAAAGGG
65 AAAATTAAAAAATATG--A-TTTTTTTAAAGTAATAAAATTCG-GGAAAAAATACGAACAAAGGG
3091901 CCGAAATAAGGG-TTTTT-TTAAATTT
126 CCGAAATAAGGGTTTTTTATTAAA--T
* * * *
3091926 ATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATTTAAAATAAT
1 -TTTAAAAAACACAATAAAATTATATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
* * *
3091991 AAAATTAGAAAATATGATATTTTTTAAAGTAACAAAATTCGGGAAAAAATACGAACAAATGGCCG
65 AAAATTAAAAAATATGAT-TTTTTTAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGGCCG
3092056 AAATAAGG
129 AAATAAGG
3092064 TTCGTTTACT
Statistics
Matches: 893, Mismatches: 104, Indels: 107
0.81 0.09 0.10
Matches are distributed among these distances:
146 38 0.04
147 12 0.01
148 9 0.01
149 66 0.07
150 40 0.04
151 126 0.14
152 230 0.26
153 102 0.11
154 62 0.07
155 103 0.12
156 46 0.05
157 57 0.06
158 2 0.00
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (150 bp):
TTTAAAAAACACAATAAAATTATATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
AAATTAAAAAATATGATTTTTTTAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGGCCGAA
ATAAGGGTTTTTTATTAAAT
Found at i:3091076 original size:12 final size:13
Alignment explanation
Indices: 3091044--3091091 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
3091034 TAATACATTT
*
3091044 CAAACATAATGTA
1 CAAAAATAATGTA
*
3091057 CTAAAATAATGTA
1 CAAAAATAATGTA
**
3091070 -AAAAATAAAATA
1 CAAAAATAATGTA
3091082 CAAAAATAAT
1 CAAAAATAAT
3091092 ATATTTTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (13 bp):
CAAAAATAATGTA
Found at i:3091545 original size:18 final size:18
Alignment explanation
Indices: 3091508--3091540 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3091498 CATAATGTAC
3091508 TAAAATAATATAAAATAA
1 TAAAATAATATAAAATAA
3091526 TAAAAT--TATAAAATA
1 TAAAATAATATAAAATA
3091541 TAATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.60
18 6 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAATAATATAAAATAA
Found at i:3093215 original size:13 final size:13
Alignment explanation
Indices: 3093197--3093240 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
3093187 GTGTTAAATT
3093197 TATATGGATGCCA
1 TATATGGATGCCA
3093210 TATATGGATG-CA
1 TATATGGATGCCA
3093222 GTTTATATGGATGCCA
1 ---TATATGGATGCCA
3093238 TAT
1 TAT
3093241 CGTCGCCCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.07
13 13 0.48
15 10 0.37
16 2 0.07
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (13 bp):
TATATGGATGCCA
Found at i:3094204 original size:77 final size:76
Alignment explanation
Indices: 3094105--3094253 Score: 253
Period size: 77 Copynumber: 1.9 Consensus size: 76
3094095 TTTATTACAC
3094105 TTTTTATAACTTAAATTGGATACAATTTAAGCATAAGCATAAGCTGAATAATTTTAATTATTCCA
1 TTTTTATAACTTAAATTGGATACAATTTAAGCATAAGCATAAGCTGAATAATTTTAATTATTCCA
3094170 AATGAATCATG
66 AATGAATCATG
* * * *
3094181 TTTTTAATACCTTAATTTGGATACAATTTAAGCATAAGTATAAGTTGAATAATTTTAATTATTCC
1 TTTTT-ATAACTTAAATTGGATACAATTTAAGCATAAGCATAAGCTGAATAATTTTAATTATTCC
3094246 AAATGAAT
65 AAATGAAT
3094254 TATACTTTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
76 5 0.07
77 63 0.93
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.40
Consensus pattern (76 bp):
TTTTTATAACTTAAATTGGATACAATTTAAGCATAAGCATAAGCTGAATAATTTTAATTATTCCA
AATGAATCATG
Found at i:3095445 original size:19 final size:19
Alignment explanation
Indices: 3095421--3095464 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3095411 TAAAAGTAAC
3095421 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
3095440 ACAACATGATTCCAAATAA
1 ACAACATCAACCCAAATAA
3095459 ACAACA
1 ACAACA
3095465 AAAATAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.27, G:0.02, T:0.14
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:3097055 original size:27 final size:29
Alignment explanation
Indices: 3096998--3097056 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3096988 TTTGTTTTAA
*
3096998 ATGTAGTGTATTTTAAAAATAAAAAATAT
1 ATGTAGTATATTTTAAAAATAAAAAATAT
3097027 ATGTAGTATATTTTAAAAATAAAAAATAT
1 ATGTAGTATATTTTAAAAATAAAAAATAT
3097056 A
1 A
3097057 GTTTTTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.37
Consensus pattern (29 bp):
ATGTAGTATATTTTAAAAATAAAAAATAT
Found at i:3097075 original size:9 final size:9
Alignment explanation
Indices: 3097061--3097098 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
3097051 AATATAGTTT
3097061 TTATTCGAA
1 TTATTCGAA
3097070 TTATTCGAA
1 TTATTCGAA
*
3097079 TTATTCGAG
1 TTATTCGAA
3097088 TTATTCGAA
1 TTATTCGAA
3097097 TT
1 TT
3097099 CGAAAATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:3098635 original size:3 final size:3
Alignment explanation
Indices: 3098629--3098672 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
3098619 AAAAAAACCA
*
3098629 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3098673 GGGTCTCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3100768 original size:3 final size:3
Alignment explanation
Indices: 3100760--3100806 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3100750 ATACTATGAC
3100760 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3100807 ATACGCTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3100992 original size:12 final size:12
Alignment explanation
Indices: 3100977--3101005 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3100967 TATGTATACC
3100977 TACATATTTTAA
1 TACATATTTTAA
3100989 TACATATTTTAA
1 TACATATTTTAA
3101001 TACAT
1 TACAT
3101006 TCATTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
TACATATTTTAA
Found at i:3102987 original size:19 final size:19
Alignment explanation
Indices: 3102947--3102988 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3102937 GTCTCTTTTC
* *
3102947 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
3102966 GCATTACATTACAT-CATAT
1 GCATT-CATTACATGCATAT
3102985 GCAT
1 GCAT
3102989 CAAACACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:3103897 original size:27 final size:27
Alignment explanation
Indices: 3103866--3103971 Score: 141
Period size: 27 Copynumber: 4.1 Consensus size: 27
3103856 ATTTTTTATG
*
3103866 AATATTGTAATGTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
*
3103893 AATATTATAATTTTGTATGAATATTG-
1 AATATTGTAATTTTGTATGAATATTGT
*
3103919 CA-ATT-T--TTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
*
3103942 AATATTGTAATTTTGTATGAATATTAT
1 AATATTGTAATTTTGTATGAATATTGT
3103969 AAT
1 AAT
3103972 GTGGGGATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
22 16 0.23
23 1 0.01
24 4 0.06
25 4 0.06
26 1 0.01
27 43 0.62
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.51
Consensus pattern (27 bp):
AATATTGTAATTTTGTATGAATATTGT
Found at i:3103926 original size:65 final size:67
Alignment explanation
Indices: 3103822--3103950 Score: 199
Period size: 65 Copynumber: 1.9 Consensus size: 67
3103812 NNNNNNNNNN
* * *
3103822 TATTGTAATATTGTAATTTTGTATGAATATTATAA-TTTTT-TATGAATATTGTAATGTTGTATG
1 TATTGTAATATTATAATTTTGTATGAATATTACAATTTTTTGTATGAATATTGTAATATTGTATG
3103885 AA
66 AA
*
3103887 TATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGTA
1 TATTGTAATATTATAATTTTGTATGAATATTACAA-TTTTTTGTATGAATATTGTAATATTGTA
3103951 ATTTTGTATG
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
65 32 0.56
67 5 0.09
68 20 0.35
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (67 bp):
TATTGTAATATTATAATTTTGTATGAATATTACAATTTTTTGTATGAATATTGTAATATTGTATG
AA
Found at i:3103935 original size:49 final size:46
Alignment explanation
Indices: 3103847--3104014 Score: 187
Period size: 49 Copynumber: 3.6 Consensus size: 46
3103837 ATTTTGTATG
* *
3103847 AATATTATAATTTTTTATGAATATTGTAATGTTGTATGAATATTGT
1 AATATTATAATTTTGTATGAATATTGCAATGTTGTATGAATATTGT
*
3103893 AATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTATAATTTTGTATGAATATTGCAA---TGTTGTATGAATATTGT
* ** **
3103942 AATATTGTAATTTTGTATGAATATTATAATG-TG-GGGATATATTGT
1 AATATTATAATTTTGTATGAATATTGCAATGTTGTATGA-ATATTGT
*
3103987 AATATTGTAATTTTTTGTATGAATATTG
1 AATATTATAA--TTTTGTATGAATATTG
3104015 TAATTATTTT
Statistics
Matches: 106, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
44 2 0.02
45 19 0.18
46 28 0.26
47 15 0.14
49 42 0.40
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (46 bp):
AATATTATAATTTTGTATGAATATTGCAATGTTGTATGAATATTGT
Found at i:3103966 original size:19 final size:19
Alignment explanation
Indices: 3103828--3103895 Score: 109
Period size: 19 Copynumber: 3.6 Consensus size: 19
3103818 NNNNTATTGT
3103828 AATATTGTAATTTTGTATG
1 AATATTGTAATTTTGTATG
* *
3103847 AATATTATAATTTTTTATG
1 AATATTGTAATTTTGTATG
*
3103866 AATATTGTAATGTTGTATG
1 AATATTGTAATTTTGTATG
3103885 AATATTGTAAT
1 AATATTGTAAT
3103896 ATTATAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.51
Consensus pattern (19 bp):
AATATTGTAATTTTGTATG
Found at i:3104102 original size:27 final size:27
Alignment explanation
Indices: 3104071--3104149 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
3104061 ATATTTTGTT
3104071 CACCATTGGCGCCTCCCAAATAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
3104098 CACCATTGGCGCCTCCCAAATAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
* *
3104125 CACCATTGGCGCCTTCCAGATAGGC
1 CACCATTGGCGCCTCCCAAATAGGC
3104150 GCCAATACTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.24, C:0.39, G:0.20, T:0.16
Consensus pattern (27 bp):
CACCATTGGCGCCTCCCAAATAGGCAC
Found at i:3106620 original size:13 final size:14
Alignment explanation
Indices: 3106576--3106624 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
3106566 TGACGAGATG
*
3106576 GAAAATGAAAAAGT
1 GAAAATGGAAAAGT
**
3106590 GAAAAT-GAAATTT
1 GAAAATGGAAAAGT
3106603 GAAAATGGAAAAGT
1 GAAAATGGAAAAGT
3106617 -AAAATGGA
1 GAAAATGGA
3106625 GAGGCTAAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.18
Consensus pattern (14 bp):
GAAAATGGAAAAGT
Found at i:3108410 original size:132 final size:132
Alignment explanation
Indices: 3107925--3108387 Score: 764
Period size: 132 Copynumber: 3.5 Consensus size: 132
3107915 GGAGCAGGTT
3107925 GATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAACCAGTAATTCTATCTCCCT
1 GATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAACCAGTAATTCTATCTCCCT
* *
3107990 GGGCAATAGTGGAATAGATCAAAGATTACAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GGGCAACAGTGGAATAGATCGAAGATTACAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
3108055 AA
131 AA
*
3108057 GATGGTGGATTTTACCTCCCTGAGGTTACAATGGAGTACATTGAAACCAGTAATTCTATCTCCCT
1 GATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAACCAGTAATTCTATCTCCCT
*
3108122 GGGCAGCAGTGGAATAGATCGAAGATTACAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GGGCAACAGTGGAATAGATCGAAGATTACAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
3108187 AA
131 AA
* *
3108189 GATGGTGGATTTTACCTCCCTGAGGTTATAGTGGAGTACATTGAAACCAGTAATTCTATCTCTCT
1 GATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAACCAGTAATTCTATCTCCCT
* * *
3108254 GGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCA
66 GGGCAACAGTGGAATAGATCGAAGATTACAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
3108319 AA
131 AA
* *** * * * * *
3108321 GCTGGCAAAATCTACCTCCCTGAGGTTGCAGTGGAGTATATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAACCAGTAATTCTATCTCCCT
3108386 GG
66 GG
3108388 TCGGCGGTGG
Statistics
Matches: 309, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 309 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
GATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAACCAGTAATTCTATCTCCCT
GGGCAACAGTGGAATAGATCGAAGATTACAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
AA
Found at i:3108567 original size:89 final size:89
Alignment explanation
Indices: 3108406--3109049 Score: 1047
Period size: 89 Copynumber: 7.2 Consensus size: 89
3108396 GGAATCAATT
* *
3108406 GAAGAAATCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTC
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
* *
3108471 CCCATACTAGTGGCAAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
* ** * *
3108495 GAAGAAAGTAGATCTTGTCTTCATGTATTACCGTGAAGTAGATCGAAGATAGCAGATCTTATCTT
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
*
3108560 CCTATACTGGTGGCGAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
* * *
3108584 GAAGAAAGCAGATCTTGTCTTCATGCACTGGCGTGAAGTAGATCAAAGATAGCAGATTTTGTCTT
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
*
3108649 CCCATACTGGTGGCGAAGTAGATT
66 CCCATACTGGTGGCGAAGTAGATC
*
3108673 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTT
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
*** * * *
3108738 CATGTACTAG-CGTGAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
* *
3108761 AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
3108826 CCCATACTGGTGGCGAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
*
3108850 GAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
* *
3108915 CCCATACTAGTGGCGAAGTAGATT
66 CCCATACTGGTGGCGAAGTAGATC
3108939 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
3109004 CCCATACTGGTGGCGAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
3109028 GAAGAAAGCAGATCTTGTCTTC
1 GAAGAAAGCAGATCTTGTCTTC
3109050 CCATACTGGT
Statistics
Matches: 508, Mismatches: 46, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
88 78 0.15
89 430 0.85
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (89 bp):
GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT
CCCATACTGGTGGCGAAGTAGATC
Found at i:3109135 original size:44 final size:44
Alignment explanation
Indices: 3109087--3109328 Score: 305
Period size: 44 Copynumber: 5.5 Consensus size: 44
3109077 ATACAAGTCT
3109087 TATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAATAATCC
** * ** *
3109131 TATCTCCCTGAAGTTGCAGTGGAGCGGATTA-AA-ACCATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGTAGA-CAGAAGAAAATA-ATCC
*
3109175 TATCTCCCTGAAGTTACAGTGGAGTAGACAGAAGAAAATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAATAATCC
* * ** *
3109219 TATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AA-ACCATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGTAGA-CAGAAGAAAATA-ATCC
3109263 TATCTCCCTG-AGTTGCAGTGGAGTAGACAGAAGAAAATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAATAATCC
3109306 TATCTCCCTGAAGTTGCAGTGGA
1 TATCTCCCTGAAGTTGCAGTGGA
3109329 ACAGATTAAA
Statistics
Matches: 165, Mismatches: 24, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
42 1 0.01
43 40 0.24
44 118 0.72
45 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAATAATCC
Found at i:3109195 original size:88 final size:88
Alignment explanation
Indices: 3109084--3109369 Score: 520
Period size: 88 Copynumber: 3.3 Consensus size: 88
3109074 AAGATACAAG
3109084 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAATAATCCTATCTCCCTGAAGTTGCA
*
3109149 GTGGAGCGGATTAAAACCATAGA
66 GTGGAGCAGATTAAAACCATAGA
*
3109172 TCTTATCTCCCTGAAGTTACAGTGGAGTAGACAGAAGAAAATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAATAATCCTATCTCCCTGAAGTTGCA
3109237 GTGGAGCAGATTAAAACCATAGA
66 GTGGAGCAGATTAAAACCATAGA
3109260 TCTTATCTCCCTG-AGTTGCAGTGGAGTAGACAGAAGAAAATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAATAATCCTATCTCCCTGAAGTTGCA
* *
3109324 GTGGAACAGATTAAAACCACAGA
66 GTGGAGCAGATTAAAACCATAGA
*
3109347 TCTTATCTCTCTGAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGT
3109370 AGAGCAGATC
Statistics
Matches: 191, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
87 83 0.43
88 108 0.57
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAATAATCCTATCTCCCTGAAGTTGCA
GTGGAGCAGATTAAAACCATAGA
Found at i:3109354 original size:44 final size:44
Alignment explanation
Indices: 3109084--3109378 Score: 298
Period size: 44 Copynumber: 6.7 Consensus size: 44
3109074 AAGATACAAG
* * **
3109084 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-CAGAAGAAAATA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AA-ACCATAGA
* *
3109128 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGA
* * * **
3109172 TCTTATCTCCCTGAAGTTACAGTGGAGTAGA-CAGAAGAAAATA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AA-ACCATAGA
*
3109216 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGA
* * **
3109260 TCTTATCTCCCTG-AGTTGCAGTGGAGTAGA-CAGAAGAAAATA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AA-ACCATAGA
* * *
3109303 TCCTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGA
* *
3109347 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
3109379 CGCATCAGAT
Statistics
Matches: 205, Mismatches: 35, Indels: 22
0.78 0.13 0.08
Matches are distributed among these distances:
42 1 0.00
43 43 0.21
44 154 0.75
45 7 0.03
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGA
Found at i:3110823 original size:3 final size:3
Alignment explanation
Indices: 3110817--3110883 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
3110807 AATTATGTTA
* *
3110817 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3110865 CAT CAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
3110884 CCTACTATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3111087 original size:12 final size:12
Alignment explanation
Indices: 3111072--3111100 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3111062 TATGTATACC
3111072 TACATATTTTAA
1 TACATATTTTAA
3111084 TACATATTTTAA
1 TACATATTTTAA
3111096 TACAT
1 TACAT
3111101 TCATTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
TACATATTTTAA
Found at i:3113095 original size:77 final size:77
Alignment explanation
Indices: 3113008--3113415 Score: 780
Period size: 77 Copynumber: 5.3 Consensus size: 77
3112998 AAAAAGTATA
*
3113008 ATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGCATCCAAATTAAGGT
1 ATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTATCCAAATTAAGGT
3113073 ATTAAAAACATG
66 ATTAAAAACATG
*
3113085 ATTCATTTGGAATAATTAAAATTATTCTGCTTATGCTTATGCTTAAATTGTATCCAAATTAAGGT
1 ATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTATCCAAATTAAGGT
3113150 ATTAAAAACATG
66 ATTAAAAACATG
3113162 ATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTATCCAAATTAAGGT
1 ATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTATCCAAATTAAGGT
3113227 ATTAAAAACATG
66 ATTAAAAACATG
*
3113239 ATTCATTTGGAATAATTAAAATTATTCTGCTTATGCTTATGCTTAAATTGTATCCAAATTAAGGT
1 ATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTATCCAAATTAAGGT
3113304 ATTAAAAACATG
66 ATTAAAAACATG
*
3113316 ATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAGTTGTATCCAAATTAAGGT
1 ATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTATCCAAATTAAGGT
3113381 ATTAAAAACATG
66 ATTAAAAACATG
3113393 ATTCATTTGGAATAATTAAAATT
1 ATTCATTTGGAATAATTAAAATT
3113416 GTATCCAATT
Statistics
Matches: 325, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 325 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.39
Consensus pattern (77 bp):
ATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTATCCAAATTAAGGT
ATTAAAAACATG
Found at i:3115909 original size:138 final size:139
Alignment explanation
Indices: 3115733--3116471 Score: 502
Period size: 153 Copynumber: 5.0 Consensus size: 139
3115723 TTTCTCGAAT
* *
3115733 TTTTTTACTTTCAATAAAAATATATTATTTTGGTATTTTATTATTTAACTTTATCTTAGTACAGT
1 TTTTTTACTTTCAATAAAAATATATTATTTT--TATTTTATTATTTTACTTTATCTTAGTACATT
* *
3115798 ATGTTTTAAATGTATTAATTAATTCTGTTTTTTTTAAATTTAGTAAAAAAACCCTTATTTCGGCC
64 ATGCTTGAAATGTATTAATTAATTCTGTTTTTTTTAAATTTAGTAAAAAAACCCTTATTTCGGCC
3115863 CTTTCTTAGTA
129 CTTTCTTAGTA
* * * * *
3115874 TTTTTTACTTT-AAAAAAAATCATATT-TTCTAATTTTATTATTTTACATTATTTTAGTACATTA
1 TTTTTTACTTTCAATAAAAAT-ATATTATTTTTATTTTATTATTTTACTTTATCTTAGTACATTA
* * ** *
3115937 TGCTTGAAAT-T-TAAATAAATT-TAGTGTGTTTTTTAAATAAATTAAAAAAACCCTTATTTCGG
65 TGCTTGAAATGTATTAATTAATTCT-GT-T-TTTTTTAAATTTAGTAAAAAAACCCTTATTTCGG
*
3115999 CCCTTTGCTTGTATTTTTTCCCGA
127 CCCTTT-C-T-TA----GT----A
3116023 TTTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTTACTTTATCTTAGTACA
1 -TTTT-TTACTTTCAATAAAAATATATTA-TTTT-TATTTTATTATTTTACTTTATCTTAGTACA
* *
3116088 TTATGCTTGAAATGTATTAATTATTTCTGTTTTTTTTTAATTTAGT-AAAAAACCCTTATTTCGG
62 TTATGCTTGAAATGTATTAATTAATTCTGTTTTTTTTAAATTTAGTAAAAAAACCCTTATTTCGG
** *
3116152 CCCTTAGTTCGTA
127 CCCTTTCTTAGTA
* * *
3116165 TTTTTTTCCCAAATTTTATTACTTTAAAAA-ATATCATATTTTGTAATTTTATTATTTTACATTA
1 -TTTTTT----ACTTTCA--A---TAAAAATATAT--TATTTT-T-ATTTTATTATTTTACTTTA
* * * * * ** *
3116229 TTTTAGTACATTATGTTTGAAAT-T-TAAATAAATT-TAGTGTGTTTTTAAAATAAATTTAAAAA
52 TCTTAGTACATTATGCTTGAAATGTATTAATTAATTCT-GT-T-TTTTTTAAATTTA-GTAAAAA
*
3116291 AACCCTTATTTCGGCCCTTTACTCGTATTTTTTCCAA
113 AACCCTTATTTCGGCCCTTT-CT--TA----GT---A
* * *
3116328 TTTTTATTACTTGCAATAAAAATATATTATTTTCGTATTTTATT-TTTTACATTATTTTAGTACA
1 -TTTT-TTACTTTCAATAAAAATATATTATTTT--TATTTTATTATTTTACTTTATCTTAGTACA
* * * * *
3116392 TCATGTTTGAAATGTATTAATT--TT-T-TCTTTTTTTAAATTTAGT-AAAAAACTCTTACTTCA
62 TTATGCTTGAAATGTATTAATTAATTCTGT-TTTTTTTAAATTTAGTAAAAAAACCCTTATTTCG
* *
3116452 GCCCTTTGTTCGTA
126 GCCCTTTCTTAGTA
3116466 TTTTTT
1 TTTTTT
3116472 TTCTCTGCAT
Statistics
Matches: 477, Mismatches: 65, Indels: 117
0.72 0.10 0.18
Matches are distributed among these distances:
135 1 0.00
136 12 0.03
137 6 0.01
138 74 0.16
139 1 0.00
140 12 0.03
141 21 0.04
142 6 0.01
145 7 0.01
146 1 0.00
147 2 0.00
148 22 0.05
149 15 0.03
150 29 0.06
151 65 0.14
152 9 0.02
153 84 0.18
154 67 0.14
155 14 0.03
156 14 0.03
157 1 0.00
158 1 0.00
160 5 0.01
163 6 0.01
164 2 0.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (139 bp):
TTTTTTACTTTCAATAAAAATATATTATTTTTATTTTATTATTTTACTTTATCTTAGTACATTAT
GCTTGAAATGTATTAATTAATTCTGTTTTTTTTAAATTTAGTAAAAAAACCCTTATTTCGGCCCT
TTCTTAGTA
Found at i:3116232 original size:305 final size:304
Alignment explanation
Indices: 3115527--3116581 Score: 1515
Period size: 305 Copynumber: 3.5 Consensus size: 304
3115517 ACTTCAAAAA
*
3115527 AAATTTAGTAAAAAACTCTTATTTCGGCCCTGTGTTCGTATTTTTTTCTGAATTTTATTACTTTA
1 AAATTTAGTAAAAAACCCTTATTTCGGCCCT-TGTTCGTATTTTTTTCTGAATTTTATTACTTTA
*
3115592 AAAATTATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAA
65 AAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAA
* *
3115657 ATAAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAACCCTTATTT-GGTCATTTGCTCGTATT
130 ATAAATTTAGTGTGTTTTTTAAATAAATTT-AAAAAAACCCTTATTTCGGCCCTTTGCTCGTA-T
* * *
3115721 TTTTTCTCGAATTTTT-TTACTTTCAATAAAAATATATTATTTTGGTATTTTATTATTTAACTTT
193 TTTTTCCCG-ATTTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACTTT
* * *
3115785 ATCTTAGTACAGTATGTTTTAAATGTATTAATTAATTCTGTTTTTTTT
257 ATCTTAGTACATTATGTTTGAAATGTATTAATTATTTCTGTTTTTTTT
* *
3115833 AAATTTAGTAAAAAAACCCTTATTTCGGCCC-T-TTC--------TT-AGTATTTT-TTACTTTA
1 AAATTTAGT-AAAAAACCCTTATTTCGGCCCTTGTTCGTATTTTTTTCTGAATTTTATTACTTTA
* *
3115886 AAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGCTTGAAATTTAA
65 AAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAA
*
3115951 ATAAATTTAGTGTGTTTTTTAAATAAA-TTAAAAAAACCCTTATTTCGGCCCTTTGCTTGTATTT
130 ATAAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTT
*
3116015 TTTCCCGATTTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTTACTTTATC
195 TTTCCCGATTTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACTTTATC
*
3116080 TTAGTACATTATGCTTGAAATGTATTAATTATTTCTGTTTTTTTT
260 TTAGTACATTATGTTTGAAATGTATTAATTATTTCTGTTTTTTTT
* **
3116125 TAATTTAGTAAAAAACCCTTATTTCGGCCCTTAGTTCGTATTTTTTTCCCAAATTTTATTACTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCCTT-GTTCGTATTTTTTT-CTGAATTTTATTACTTT
*
3116190 AAAAAATATCATATTTTGTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA
64 AAAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA
* *
3116255 AATAAATTTAGTGTGTTTTTAAAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTACTCGTATT
129 AATAAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGCTCGTATT
* * *
3116320 TTTT-CCAATTTTTATTACTTGCAATAAAAATATATTATTTTCGTATTTTATT-TTTTACATTAT
194 TTTTCCCGATTTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACTTTAT
* * *
3116383 TTTAGTACATCATGTTTGAAATGTATTAATT-TTT-T-CTTTTTTT
259 CTTAGTACATTATGTTTGAAATGTATTAATTATTTCTGTTTTTTTT
* * * *
3116426 AAATTTAGTAAAAAACTCTTACTTCAGCCCTTTGTTCGTATTTTTTTTCTCTGCATTTTATTACT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCC-TTGTTCGTA--TTTTTT-TCTGAATTTTATTACT
* * * *
3116491 TTAAAAAATATAATGTTTTCTAATTTTATTATTTTACATTATTTTATTTCATTATGTTTGAAATT
62 TTAAAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
*
3116556 T--ATTAATTTAGTGTGTTTTTTAAATA
127 TAAATAAATTTAGTGTGTTTTTTAAATA
3116582 TACAATTTTT
Statistics
Matches: 679, Mismatches: 48, Indels: 49
0.88 0.06 0.06
Matches are distributed among these distances:
291 27 0.04
292 124 0.18
293 14 0.02
294 100 0.15
295 6 0.01
296 2 0.00
301 63 0.09
302 5 0.01
303 82 0.12
304 47 0.07
305 142 0.21
306 47 0.07
307 20 0.03
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (304 bp):
AAATTTAGTAAAAAACCCTTATTTCGGCCCTTGTTCGTATTTTTTTCTGAATTTTATTACTTTAA
AAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAA
TAAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTT
TTCCCGATTTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACTTTATCT
TAGTACATTATGTTTGAAATGTATTAATTATTTCTGTTTTTTTT
Found at i:3116954 original size:34 final size:34
Alignment explanation
Indices: 3116914--3117021 Score: 105
Period size: 38 Copynumber: 3.0 Consensus size: 34
3116904 TACTTCTTTT
3116914 TTTCCTTTCTTTTTCCTTCCTTC-CCTTTTCTTC
1 TTTCCTTTCTTTTTCCTTCCTTCTCCTTTTCTTC
* *
3116947 TTCTCCTTTTTTTTTCTCTTTCTTCTCCTTCCTT-TTC
1 TT-TCCTTTCTTTTTC-CTTCCTTCTCCTT--TTCTTC
3116984 TTT-CTTTCTTTCCTCTCCTTTCCTTCTCCTTTTCTTC
1 TTTCCTTTCTTT--T-TCC-TTCCTTCTCCTTTTCTTC
3117021 T
1 T
3117022 CCACCCACCG
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
33 2 0.03
34 12 0.20
35 14 0.23
36 7 0.11
37 11 0.18
38 15 0.25
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (34 bp):
TTTCCTTTCTTTTTCCTTCCTTCTCCTTTTCTTC
Found at i:3116963 original size:13 final size:14
Alignment explanation
Indices: 3116933--3116985 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 14
3116923 TTTTTCCTTC
3116933 CTTC-CCTTTTCTT
1 CTTCTCCTTTTCTT
3116946 CTTCTCCTTTT-TT
1 CTTCTCCTTTTCTT
*
3116959 TTTCT-C-TTTCTT
1 CTTCTCCTTTTCTT
*
3116971 CTCCTTCCTTTTCTT
1 CTTC-TCCTTTTCTT
3116986 TCTTTCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
11 3 0.09
12 5 0.16
13 11 0.34
14 7 0.22
15 6 0.19
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (14 bp):
CTTCTCCTTTTCTT
Found at i:3116969 original size:25 final size:27
Alignment explanation
Indices: 3116941--3117008 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
3116931 TCCTTCCCTT
*
3116941 TTCTTCTTC-TCCTTTT-TTT-TTCTCT
1 TTCTTCTCCTTCCTTTTCTTTCTT-TCT
3116966 TTCTTCTCCTTCCTTTTCTTTCTTTCT
1 TTCTTCTCCTTCCTTTTCTTTCTTTCT
*
3116993 TTCCTCTCCTTTCCTT
1 TTCTTCTCC-TTCCTT
3117009 CTCCTTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.22
26 7 0.19
27 14 0.38
28 8 0.22
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (27 bp):
TTCTTCTCCTTCCTTTTCTTTCTTTCT
Found at i:3116986 original size:19 final size:19
Alignment explanation
Indices: 3116931--3117014 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
3116921 TCTTTTTCCT
3116931 TCCTTCCCTTTTC-TTCTTC
1 TCCTT-CCTTTTCTTTCTTC
**
3116950 TCCTTTTTTTTTCTCTTTCTTC
1 TCC--TTCCTTT-TCTTTCTTC
3116972 TCCTTCCTTTTCTTTCTT-
1 TCCTTCCTTTTCTTTCTTC
* * *
3116990 TCTTTCCTCTCCTTTCCTTC
1 TCCTTCCTTTTCTTT-CTTC
3117010 TCCTT
1 TCCTT
3117015 TTCTTCTCCA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
18 12 0.24
19 14 0.27
20 12 0.24
21 4 0.08
22 9 0.18
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (19 bp):
TCCTTCCTTTTCTTTCTTC
Found at i:3116993 original size:45 final size:44
Alignment explanation
Indices: 3116901--3116997 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 44
3116891 AAAAAATTAC
* *
3116901 CTTTACTTCTTTTTTTCCTTTCTTTTTCCTTCCTTCCCTTTTCTT
1 CTTTCCTT-TTTTTTTCCTTTCTTTCTCCTTCCTTCCCTTTTCTT
**
3116946 CTTCTCCTTTTTTTTTCTCTTTC-TTCTCCTTCCTTTTC-TTTCTTT
1 CTT-TCCTTTTTTTTTC-CTTTCTTTCTCCTTCCTTCCCTTTTC-TT
3116991 CTTTCCT
1 CTTTCCT
3116998 CTCCTTTCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
44 8 0.18
45 28 0.62
46 9 0.20
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (44 bp):
CTTTCCTTTTTTTTTCCTTTCTTTCTCCTTCCTTCCCTTTTCTT
Found at i:3117006 original size:10 final size:11
Alignment explanation
Indices: 3116916--3117023 Score: 54
Period size: 11 Copynumber: 10.3 Consensus size: 11
3116906 CTTCTTTTTT
* *
3116916 TCCTTTCTTTT
1 TCCTTTCCTTC
3116927 TCC-TTCCTTC
1 TCCTTTCCTTC
3116937 -CCTTTTCTTCTTC
1 TCC-TTTC--CTTC
** *
3116950 TCCTTTTTTTT
1 TCCTTTCCTTC
3116961 TCTCTTT-CTTC
1 TC-CTTTCCTTC
3116972 TCC-TTCCTT-
1 TCCTTTCCTTC
*
3116981 TTCTTT-CTT-
1 TCCTTTCCTTC
3116990 T-CTTTCC-TC
1 TCCTTTCCTTC
3116999 TCCTTTCCTTC
1 TCCTTTCCTTC
*
3117010 TCCTTTTCTTC
1 TCCTTTCCTTC
3117021 TCC
1 TCC
3117024 ACCCACCGGG
Statistics
Matches: 76, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
8 5 0.07
9 12 0.16
10 17 0.22
11 29 0.38
12 4 0.05
13 7 0.09
14 2 0.03
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (11 bp):
TCCTTTCCTTC
Found at i:3123733 original size:14 final size:14
Alignment explanation
Indices: 3123701--3123743 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3123691 AAAATTATTA
3123701 AAATTTTAAAAATC
1 AAATTTTAAAAATC
*
3123715 TAATTTTAAAATAT-
1 AAATTTTAAAA-ATC
*
3123729 AAATTATAAAAATC
1 AAATTTTAAAAATC
3123743 A
1 A
3123744 TAAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.08
14 20 0.83
15 2 0.08
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATTTTAAAAATC
Found at i:3126097 original size:20 final size:21
Alignment explanation
Indices: 3126061--3126103 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3126051 TTAATGTCTT
3126061 ATAATTGTTTATAAATTTATA
1 ATAATTGTTTATAAATTTATA
* *
3126082 ATAATT-TTTATGAATTTTTA
1 ATAATTGTTTATAAATTTATA
3126102 AT
1 AT
3126104 TTATATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATAATTGTTTATAAATTTATA
Found at i:3126848 original size:30 final size:29
Alignment explanation
Indices: 3126813--3126880 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
3126803 TTAGCCAATC
3126813 GGTGATTAAAAAGATAAAATTA-AATAATTG
1 GGTGATTAAAAA-A-AAAATTATAATAATTG
* *
3126843 GGTGATCAAAAAAAAATTTATTAATAATTG
1 GGTGATTAAAAAAAAAATTA-TAATAATTG
*
3126873 GATGATTA
1 GGTGATTA
3126881 CTAATGTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.19
29 1 0.03
30 25 0.78
ACGTcount: A:0.50, C:0.01, G:0.16, T:0.32
Consensus pattern (29 bp):
GGTGATTAAAAAAAAAATTATAATAATTG
Found at i:3129527 original size:20 final size:20
Alignment explanation
Indices: 3129473--3129528 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
3129463 TTTATGTTTT
*
3129473 CATATAGTTTTTATATACATA
1 CATATA-TTTTTATACACATA
*
3129494 CATAT-TCTTATATACACATA
1 CATATAT-TTTTATACACATA
3129514 CATATATTTTTATAC
1 CATATATTTTTATAC
3129529 TTTATAATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 23 0.77
21 6 0.20
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (20 bp):
CATATATTTTTATACACATA
Found at i:3130823 original size:18 final size:19
Alignment explanation
Indices: 3130782--3130825 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
3130772 TTACACTAAC
3130782 AAATAATTTAAAAGTTATAA
1 AAAT-ATTTAAAAGTTATAA
3130802 AAATATTTAAAA-TTCA-AA
1 AAATATTTAAAAGTT-ATAA
3130820 AAATAT
1 AAATAT
3130826 ATGATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.43
19 9 0.39
20 4 0.17
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATATTTAAAAGTTATAA
Found at i:3134075 original size:13 final size:13
Alignment explanation
Indices: 3134059--3134089 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3134049 GTATAAAATT
3134059 ATTTAAAATTAAA
1 ATTTAAAATTAAA
*
3134072 ATTTAAAATTTAA
1 ATTTAAAATTAAA
3134085 ATTTA
1 ATTTA
3134090 TACAAATAAA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTAAAATTAAA
Found at i:3138350 original size:23 final size:22
Alignment explanation
Indices: 3138318--3138379 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
3138308 CCCGGCCCGC
*
3138318 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
3138342 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
3138364 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
3138380 TTGTTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:3138374 original size:16 final size:16
Alignment explanation
Indices: 3138353--3138409 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
3138343 TTTTATTAAA
*
3138353 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
3138369 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
* *
3138385 ATCAAAATTAATTATT
1 ATTAAAATTAATTGTT
3138401 ATTAAAATT
1 ATTAAAATT
3138410 GTATCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:3138551 original size:86 final size:90
Alignment explanation
Indices: 3138455--3138631 Score: 263
Period size: 93 Copynumber: 2.0 Consensus size: 90
3138445 TTTGTAAAAT
* *
3138455 CTAACATTTTGTTAGT-AAA-ATT-A-TTAATTGTATTAATTGTTACTAAAATTATCAAATTATA
1 CTAACATTTTGTTAGTAAAATATTAATTTAATTGTATTAATTATTACTAAAATTATCAAATTACA
3138516 TCAAATTATTAATTATTAATTGTTA
66 TCAAATTATTAATTATTAATTGTTA
*
3138541 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTATTAGTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAA-TATTAA-T-TTAATTGTATTAATTATTACTAAAATTATCAAATT
*
3138606 ACATCAAATTATTAATTGTTAATTGT
63 ACATCAAATTATTAATTATTAATTGT
3138632 ATTAATTGTT
Statistics
Matches: 80, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
86 16 0.20
87 3 0.04
89 3 0.04
90 1 0.01
93 57 0.71
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (90 bp):
CTAACATTTTGTTAGTAAAATATTAATTTAATTGTATTAATTATTACTAAAATTATCAAATTACA
TCAAATTATTAATTATTAATTGTTA
Found at i:3145081 original size:44 final size:45
Alignment explanation
Indices: 3145032--3145134 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 45
3145022 TGGTTTTAGT
*
3145032 CTGCTCCACTGCAA-TGTTAGGGAGATAAGACTTG-TAACTCCAAC
1 CTGCTCCACTGCAATTG-TAGGGAGACAAGACTTGCTAACTCCAAC
* * ** *
3145076 CTGCTCCACTGCAATTGTAGGGAGACCAGATTTGCTGTCTTCAAC
1 CTGCTCCACTGCAATTGTAGGGAGACAAGACTTGCTAACTCCAAC
3145121 CTGCTCCACTGCAA
1 CTGCTCCACTGCAA
3145135 CTTCAGAGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
44 28 0.55
45 23 0.45
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (45 bp):
CTGCTCCACTGCAATTGTAGGGAGACAAGACTTGCTAACTCCAAC
Found at i:3145152 original size:45 final size:44
Alignment explanation
Indices: 3145032--3145331 Score: 146
Period size: 45 Copynumber: 6.7 Consensus size: 44
3145022 TGGTTTTAGT
* * * *
3145032 CTGCTCCACTGCAA-TGTTAGGGAGATAAGACTTGTAACTCCAAC
1 CTGCTCCACTGCAACT-TCAGGGAGATAAGATTTGTATCTTCAAC
* ** *
3145076 CTGCTCCACTGCAA-TTGTAGGGAGACCAGATTTGCTGTCTTCAAC
1 CTGCTCCACTGCAACTT-CAGGGAGATAAGATTTG-TATCTTCAAC
* ** **
3145121 CTGCTCCACTGCAACTTCAGAGAGATAAGATTCACTATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGTATCTTCAAC
* * * * * *
3145166 CTACTCCACTACAACTTCAGGGAGATAATATTT-TAT-AT-GAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAAC
* * * * * * * *
3145207 CTGCTCTACTGCAATTTTAGAGATATTAGATCTGCAATTTATAGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGA-TA-A---G--ATTTGTATCTTCAAC
* **
3145258 CTGTTCCACTGC-ACTTCAGGG-GAATAAGATTTGCTATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAG-ATAAGATTTG-TATCTTCAAC
* *
3145302 TTGCTCCACTGCAACTTTAGGGAGATAAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA
3145332 CTTACTATGG
Statistics
Matches: 192, Mismatches: 46, Indels: 35
0.70 0.17 0.13
Matches are distributed among these distances:
41 19 0.10
42 3 0.02
43 9 0.05
44 47 0.24
45 82 0.43
46 3 0.02
48 5 0.03
49 4 0.02
50 8 0.04
51 12 0.06
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAAC
Found at i:3146438 original size:20 final size:19
Alignment explanation
Indices: 3146398--3146442 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3146388 AAAATACTTG
* *
3146398 AAAATT-AAAAAGATATTA
1 AAAATTCAAAAAAATATAA
3146416 AAAATTCAAAAAAATTATAA
1 AAAATTCAAAAAAA-TATAA
3146436 AAAATTC
1 AAAATTC
3146443 CCCAAATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 11 0.48
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATTCAAAAAAATATAA
Found at i:3146549 original size:25 final size:25
Alignment explanation
Indices: 3146516--3146569 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
3146506 GTTTTAATAT
3146516 TTTTGTGGAATTTATAAAACTATGA
1 TTTTGTGGAATTTATAAAACTATGA
3146541 TTTTGTGGAATTTATAAAACTATGA
1 TTTTGTGGAATTTATAAAACTATGA
3146566 TTTT
1 TTTT
3146570 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (25 bp):
TTTTGTGGAATTTATAAAACTATGA
Found at i:3146583 original size:26 final size:25
Alignment explanation
Indices: 3146524--3146579 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3146514 ATTTTTGTGG
**
3146524 AATTTATAAAACTATGATTTTGTGG
1 AATTTATAAAACTATGATTTTGTAA
*
3146549 AATTTATAAAACTATGATTTTTTAA
1 AATTTATAAAACTATGATTTTGTAA
3146574 AATTTA
1 AATTTA
3146580 ATAAGTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (25 bp):
AATTTATAAAACTATGATTTTGTAA
Found at i:3159483 original size:29 final size:31
Alignment explanation
Indices: 3159447--3159507 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
3159437 AAACCTTTTT
* *
3159447 ACTTTTCCCTCAAAACTTTTACTCCT-TCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
3159477 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
3159508 CTCCCAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
Found at i:3159646 original size:30 final size:31
Alignment explanation
Indices: 3159612--3159671 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
3159602 AAACCTTTTA
*
3159612 TTTTCCCCCAAAATTTTTATT-CCTTCCCAC
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
*
3159642 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCA
3159672 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
Found at i:3159789 original size:17 final size:16
Alignment explanation
Indices: 3159754--3159785 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3159744 CCCTAATTAC
*
3159754 ATTCCCTCAAACTTTT
1 ATTCCCTAAAACTTTT
3159770 ATTCCCTAAAACTTTT
1 ATTCCCTAAAACTTTT
3159786 TATTTTCCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTCCCTAAAACTTTT
Found at i:3159811 original size:20 final size:21
Alignment explanation
Indices: 3159773--3159817 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3159763 AACTTTTATT
*
3159773 CCCTAAAACTTTTTATTTTCC
1 CCCTAAAACTTTTTATTTTCA
3159794 CCCT-AAAC-TTTTACTTTTCA
1 CCCTAAAACTTTTTA-TTTTCA
3159814 CCCT
1 CCCT
3159818 TTACTCTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 13 0.59
21 4 0.18
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (21 bp):
CCCTAAAACTTTTTATTTTCA
Found at i:3159948 original size:17 final size:17
Alignment explanation
Indices: 3159928--3159974 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3159918 CACATTTTAT
3159928 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
3159945 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTGA
3159963 A-TATTTATATTA
1 ATTATTTATATTA
3159975 AAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 14 0.52
18 8 0.30
19 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:3160112 original size:19 final size:19
Alignment explanation
Indices: 3160068--3160113 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
3160058 CTTTTATTAA
3160068 AAAATCATATTTTTACATTT
1 AAAAT-ATATTTTTACATTT
3160088 --AATATATTTTTA-ATTCT
1 AAAATATATTTTTACATT-T
3160105 AAAATATAT
1 AAAATATAT
3160114 AGTGACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.13
17 10 0.43
18 3 0.13
19 7 0.30
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATATATTTTTACATTT
Found at i:3160946 original size:17 final size:17
Alignment explanation
Indices: 3160924--3160963 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3160914 ATTAATGAAA
3160924 ACAAATTGTC-AATAGAT
1 ACAAATTGTCTAAT-GAT
3160941 ACAAATTGTCTAATGAT
1 ACAAATTGTCTAATGAT
3160958 ACAAAT
1 ACAAAT
3160964 CTAGGACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (17 bp):
ACAAATTGTCTAATGAT
Found at i:3163349 original size:13 final size:13
Alignment explanation
Indices: 3163331--3163357 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3163321 ACAACACCCA
3163331 ACTTATAACCACC
1 ACTTATAACCACC
3163344 ACTTATAACCACC
1 ACTTATAACCACC
3163357 A
1 A
3163358 TTAAAGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (13 bp):
ACTTATAACCACC
Found at i:3165073 original size:18 final size:18
Alignment explanation
Indices: 3165050--3165114 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
3165040 TTAACTTTTT
3165050 TATTTTTAAATTTTAATA
1 TATTTTTAAATTTTAATA
* *
3165068 TATTTTTTATTTTTAA-A
1 TATTTTTAAATTTTAATA
*
3165085 -A-TTTTAATATTTTTTATA
1 TATTTTTAA-A-TTTTAATA
3165103 TATTTTTTAAAT
1 TA-TTTTTAAAT
3165115 AATATTATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
15 5 0.14
16 1 0.03
17 6 0.17
18 15 0.42
19 2 0.06
20 1 0.03
21 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTTAAATTTTAATA
Found at i:3165073 original size:24 final size:25
Alignment explanation
Indices: 3165045--3165108 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 25
3165035 TTAATTTAAC
3165045 TTTTTTATTTTT-AAATTTTAATAT
1 TTTTTTATTTTTAAAATTTTAATAT
3165069 ATTTTTTATTTTTAAAATTTTAATAT
1 -TTTTTTATTTTTAAAATTTTAATAT
3165095 TTTTTATATATTTT
1 TTTTT-TAT-TTTT
3165109 TTAAATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
25 17 0.47
26 15 0.42
27 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTTATTTTTAAAATTTTAATAT
Found at i:3165081 original size:26 final size:26
Alignment explanation
Indices: 3165045--3165114 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
3165035 TTAATTTAAC
3165045 TTTTTTA-TTTTTAAATTTTAATATA
1 TTTTTTATTTTTTAAATTTTAATATA
* *
3165070 TTTTTTATTTTTAAAATTTTAATATT
1 TTTTTTATTTTTTAAATTTTAATATA
3165096 TTTTATATATTTTTTAAAT
1 TTTT-T-TATTTTTTAAAT
3165115 AATATTATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
25 7 0.18
26 20 0.51
27 1 0.03
28 11 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTTTTATTTTTTAAATTTTAATATA
Found at i:3165794 original size:123 final size:123
Alignment explanation
Indices: 3165638--3165882 Score: 341
Period size: 123 Copynumber: 2.0 Consensus size: 123
3165628 TATTTGAATT
* * * * *
3165638 TTAGTCTTCATAATCTTATTTTTAGAAATTTAATCAACTTCTTTTCGGATTTAAAAATTTAGGAT
1 TTAGTCTTCATAATCTTATTTTTAAAAATTTAATCAACTACTTTTCAGATTTAAAAATTCAGGAC
* * * *
3165703 CTATTATTACCACTGTTAATATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAAC
66 CCATTATTACCACCGTTAAAATTCCTCTATTAAATTCATTGGTGTGACGTTTTGGAAC
* * *
3165761 TTAGT-TTCCATACTCTTA-TTTTAAATAATTTAATTATCTACTTTTCAGATTTAAAAATTCAGG
1 TTAGTCTT-CATAATCTTATTTTTAAA-AATTTAATCAACTACTTTTCAGATTTAAAAATTCAGG
*
3165824 ACCCATTATTATCACCGTTAAAATTCCTCTATTAAATTCATTGGTGTGACGTTTTGGAA
64 ACCCATTATTACCACCGTTAAAATTCCTCTATTAAATTCATTGGTGTGACGTTTTGGAA
3165883 TTTAAAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
122 8 0.07
123 99 0.93
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (123 bp):
TTAGTCTTCATAATCTTATTTTTAAAAATTTAATCAACTACTTTTCAGATTTAAAAATTCAGGAC
CCATTATTACCACCGTTAAAATTCCTCTATTAAATTCATTGGTGTGACGTTTTGGAAC
Found at i:3171319 original size:35 final size:35
Alignment explanation
Indices: 3171278--3171347 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
3171268 TTTAATGAAT
3171278 TTAATATTAAATTAAATTTAATATTTATCTAGATA
1 TTAATATTAAATTAAATTTAATATTTATCTAGATA
* * *
3171313 TTAATATTATATTTAATTTAGTATTTATCTAGATA
1 TTAATATTAAATTAAATTTAATATTTATCTAGATA
3171348 ATATTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (35 bp):
TTAATATTAAATTAAATTTAATATTTATCTAGATA
Found at i:3171337 original size:17 final size:17
Alignment explanation
Indices: 3171275--3171337 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
3171265 TGTTTTAATG
* *
3171275 AATTTAATATTAAATTA
1 AATTTAATATTATATTT
*
3171292 AATTTAATATT-TATCT
1 AATTTAATATTATATTT
3171308 AGATATTAATATTATATTT
1 A-AT-TTAATATTATATTT
*
3171327 AATTTAGTATT
1 AATTTAATATT
3171338 TATCTAGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 3 0.08
17 20 0.53
18 10 0.26
19 5 0.13
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTAATATTATATTT
Found at i:3171933 original size:38 final size:38
Alignment explanation
Indices: 3171874--3171988 Score: 135
Period size: 38 Copynumber: 3.0 Consensus size: 38
3171864 ACCTCGAAGA
* * * *
3171874 TTTGAAATGTTGA-ACAGATCTTCCCTCTATCTTGATGC
1 TTTGAAGTGTTGAGAGA-ATCTTCCCACCATCTTGATGC
* *
3171912 TTTGAAGTGTT-AGGAGAATCTTGCCACCATCTTGAAGC
1 TTTGAAGTGTTGA-GAGAATCTTCCCACCATCTTGATGC
*
3171950 TTTGAAGTGTTGAGCGAATCTTCCCACCATCTTGATGC
1 TTTGAAGTGTTGAGAGAATCTTCCCACCATCTTGATGC
3171988 T
1 T
3171989 ACTAAGGGTT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
37 1 0.02
38 61 0.94
39 3 0.05
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (38 bp):
TTTGAAGTGTTGAGAGAATCTTCCCACCATCTTGATGC
Found at i:3172000 original size:38 final size:38
Alignment explanation
Indices: 3171927--3172039 Score: 106
Period size: 38 Copynumber: 3.0 Consensus size: 38
3171917 AGTGTTAGGA
* * * *
3171927 GAATCTTGCCACCATCTTGAAGCT-TTGAAGTGTTGAGC
1 GAATCTTCCCACCATCTTGATGCTACT-AAGAGTTGAGC
*
3171965 GAATCTTCCCACCATCTTGATGCTACTAAGGGTTGA-C
1 GAATCTTCCCACCATCTTGATGCTACTAAGAGTTGAGC
* * * *
3172002 TAGA-CTTCCCACCTTATTGATGCTACAAAGAGTTGAGC
1 GA-ATCTTCCCACCATCTTGATGCTACTAAGAGTTGAGC
3172040 AAATTTCTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
37 30 0.48
38 32 0.51
39 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (38 bp):
GAATCTTCCCACCATCTTGATGCTACTAAGAGTTGAGC
Found at i:3177597 original size:33 final size:33
Alignment explanation
Indices: 3177560--3177627 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
3177550 AATGGAAAGT
3177560 CTCCATATGAGATGTTGTACAAATCTGTGCTTG
1 CTCCATATGAGATGTTGTACAAATCTGTGCTTG
3177593 CTCCATATGAGATGTTGTACAAATCTGTGCTTG
1 CTCCATATGAGATGTTGTACAAATCTGTGCTTG
3177626 CT
1 CT
3177628 TACATGTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (33 bp):
CTCCATATGAGATGTTGTACAAATCTGTGCTTG
Found at i:3179820 original size:20 final size:18
Alignment explanation
Indices: 3179792--3179840 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
3179782 GATTTTAAAA
*
3179792 TAGTAGTTAACAGTTATAGT
1 TAGTTGTTAACAG-T-TAGT
*
3179812 TAGTTGTTAGCAGTTAGT
1 TAGTTGTTAACAGTTAGT
*
3179830 TAGTTGATAAC
1 TAGTTGTTAAC
3179841 TGGTACTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 13 0.52
19 1 0.04
20 11 0.44
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (18 bp):
TAGTTGTTAACAGTTAGT
Found at i:3181532 original size:35 final size:36
Alignment explanation
Indices: 3181453--3181533 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
3181443 ATATATGTGG
*
3181453 ATATATATG--TATGTGAATTATAAAATATACGAAAA
1 ATATATATGTATATATGAATTATAAAATATAC-AAAA
* *
3181488 ATATGTATGTATATATGAATTATGAAATATA-AAAA
1 ATATATATGTATATATGAATTATAAAATATACAAAA
*
3181523 CTATATATGTA
1 ATATATATGTA
3181534 AAAGAGGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
35 21 0.54
37 18 0.46
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.37
Consensus pattern (36 bp):
ATATATATGTATATATGAATTATAAAATATACAAAA
Found at i:3181780 original size:5 final size:5
Alignment explanation
Indices: 3181772--3181820 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
3181762 AAAAATAAAA
* *
3181772 ATAAT ATAAT ATAAT ATAAT ATAAGCA ATTAT ATAAT AATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAA--T ATAAT ATAAT -ATAAT ATAAT
3181820 A
1 A
3181821 AGATACATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 29 0.78
6 5 0.14
7 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:3181877 original size:3 final size:3
Alignment explanation
Indices: 3181871--3181904 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3181861 AAATATGATG
*
3181871 ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3181905 CAATCACAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:3181885 original size:9 final size:9
Alignment explanation
Indices: 3181871--3181908 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
3181861 AAATATGATG
3181871 ATAATAACA
1 ATAATAACA
*
3181880 ATAATAATA
1 ATAATAACA
*
3181889 ATAATAATA
1 ATAATAACA
3181898 ATAATAACA
1 ATAATAACA
3181907 AT
1 AT
3181909 CACAGGACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (9 bp):
ATAATAACA
Found at i:3182471 original size:17 final size:18
Alignment explanation
Indices: 3182449--3182488 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
3182439 TTGAAATAAA
3182449 AATAAAATAAA-ATAAT-G
1 AATAAAATAAACA-AATCG
3182466 AAT-AAATAAACAAATCG
1 AATAAAATAAACAAATCG
3182483 AATAAA
1 AATAAA
3182489 GGACCTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 10 0.50
17 8 0.40
18 2 0.10
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (18 bp):
AATAAAATAAACAAATCG
Found at i:3183959 original size:42 final size:41
Alignment explanation
Indices: 3183888--3183972 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 41
3183878 TTAATATTTT
* *
3183888 AATCAATATTTTCATTAGAAATAACAATTCAACTCTTTTTGA
1 AATCAATATTTTCATCAGAAACAACAATTCAACT-TTTTTGA
* *
3183930 AATCAATATTTTCATCAGAAGCAATAATTCAACTTTTTTGA
1 AATCAATATTTTCATCAGAAACAACAATTCAACTTTTTTGA
3183971 AA
1 AA
3183973 GCTTGAGCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 9 0.23
42 30 0.77
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (41 bp):
AATCAATATTTTCATCAGAAACAACAATTCAACTTTTTTGA
Found at i:3186779 original size:28 final size:28
Alignment explanation
Indices: 3186745--3186800 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
3186735 GGGGAATAAT
*
3186745 TTGAAATTATTCAAATTTCCTTGAATTA
1 TTGAAATTATTCAAATTTCCTTAAATTA
*
3186773 TTGAAATTATTTAAATTTCCTTAAATTA
1 TTGAAATTATTCAAATTTCCTTAAATTA
3186801 ACTGAGTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (28 bp):
TTGAAATTATTCAAATTTCCTTAAATTA
Done.