Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 100 of 187
Found at i:29228712 original size:16 final size:17
Alignment explanation
Indices: 29228649--29228730 Score: 61
Period size: 17 Copynumber: 5.0 Consensus size: 17
29228639 TATTCAAGTT
29228649 ATTATAAATATTATATCT-
1 ATTAT-AATATTATAT-TA
29228667 A-TATAATTATTATAATT-
1 ATTATAA-TATTAT-ATTA
29228684 ATTAT--TATT-TATTA
1 ATTATAATATTATATTA
*
29228698 ATTGTAAT-TTATATTA
1 ATTATAATATTATATTA
*
29228714 ATTATATTATTATATTA
1 ATTATAATATTATATTA
29228731 TGGAATAAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
13 3 0.06
14 5 0.09
15 6 0.11
16 14 0.26
17 19 0.36
18 6 0.11
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (17 bp):
ATTATAATATTATATTA
Found at i:29229908 original size:3 final size:3
Alignment explanation
Indices: 29229900--29229934 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29229890 GTGAGGTAAG
29229900 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29229935 GTGAGAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29230100 original size:23 final size:22
Alignment explanation
Indices: 29230074--29230139 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
29230064 TGTGAATTTG
* *
29230074 TGGATTAATTATTGATTGAAAGC
1 TGGATAAATTATTGATTGAAA-A
* *
29230097 TGGAAAAATGATTGAATTGAAAA
1 TGGATAAATTATTG-ATTGAAAA
29230120 TGTGATAAATTA-TGATTGAA
1 TG-GATAAATTATTGATTGAA
29230140 TTGGAGTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 6 0.17
23 15 0.43
24 14 0.40
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (22 bp):
TGGATAAATTATTGATTGAAAA
Found at i:29230337 original size:37 final size:38
Alignment explanation
Indices: 29230287--29230377 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 38
29230277 CGGATAGTTT
* * *
29230287 CGATGAGGTACTGGGTACCAACTTT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTACCAACTTTGCTTCGAACTAT-C
* **
29230324 CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTATC
1 CGATGAGGCACTGGGTACCAACTTTGCTTCGAACTATC
29230362 CGATGAGGCACTGGGT
1 CGATGAGGCACTGGGT
29230378 GCCATTCTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 21 0.47
38 21 0.47
39 3 0.07
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (38 bp):
CGATGAGGCACTGGGTACCAACTTTGCTTCGAACTATC
Found at i:29230354 original size:38 final size:37
Alignment explanation
Indices: 29230287--29230381 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 37
29230277 CGGATAGTTT
* * * *
29230287 CGATGAGGTACTGGGTACCAACTTTCTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTTTCTTCGAACTAT-C
* *
29230324 CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTTT-CTTCGAACTATC
29230362 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
29230382 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
37 21 0.44
38 24 0.50
39 3 0.06
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.27
Consensus pattern (37 bp):
CGATGAGGCACTGGGTGCCAACTTTCTTCGAACTATC
Found at i:29233725 original size:20 final size:20
Alignment explanation
Indices: 29233685--29233728 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
29233675 GACGTGTTAC
* *
29233685 AATGAAAAAGAAGAGAAAAA
1 AATGAAAAAGAAAACAAAAA
*
29233705 AATGAAAAAGAAAACAGAAA
1 AATGAAAAAGAAAACAAAAA
29233725 AATG
1 AATG
29233729 GAGAGAGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (20 bp):
AATGAAAAAGAAAACAAAAA
Found at i:29237692 original size:32 final size:32
Alignment explanation
Indices: 29237651--29237711 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
29237641 CAAATCACAC
29237651 TTCCTTTGCTTTTGCTTTTGTTTTTAGCTAAA
1 TTCCTTTGCTTTTGCTTTTGTTTTTAGCTAAA
29237683 TTCCTTTGCTTTTGCTTTTGTTTTTAGCT
1 TTCCTTTGCTTTTGCTTTTGTTTTTAGCT
29237712 TTTAGATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.08, C:0.16, G:0.13, T:0.62
Consensus pattern (32 bp):
TTCCTTTGCTTTTGCTTTTGTTTTTAGCTAAA
Found at i:29238975 original size:28 final size:27
Alignment explanation
Indices: 29238922--29238976 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
29238912 GTTCGACATC
*
29238922 AAAAGATATTTTTAATTAAAATTAAAT
1 AAAAGATATTTTTAATTAAAAGTAAAT
29238949 AAAA-ATATTTTTAAATTAAAAAGTAAAT
1 AAAAGATATTTTT-AATT-AAAAGTAAAT
29238977 CCAAGTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 8 0.32
28 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
AAAAGATATTTTTAATTAAAAGTAAAT
Found at i:29241117 original size:16 final size:15
Alignment explanation
Indices: 29241094--29241127 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29241084 CCCTAAGTGT
*
29241094 TGAAAATTTAAGTAC
1 TGAAAAATTAAGTAC
*
29241109 TGAAAAATTAAGTAT
1 TGAAAAATTAAGTAC
29241124 TGAA
1 TGAA
29241128 TTTAAGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.32
Consensus pattern (15 bp):
TGAAAAATTAAGTAC
Found at i:29245937 original size:41 final size:41
Alignment explanation
Indices: 29245878--29245956 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
29245868 GCCAGATGAC
* * *
29245878 TGTGTGCCAAACCGTGTGAGCCATAAGGGCGTGTGTCTGGT
1 TGTGTGCCAAACCATGTGAGACACAAGGGCGTGTGTCTGGT
* * *
29245919 TGTGTGTCAGACCATGTGAGACACACGGGCGTGTGTCT
1 TGTGTGCCAAACCATGTGAGACACAAGGGCGTGTGTCT
29245957 AGCTGCATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.35, T:0.27
Consensus pattern (41 bp):
TGTGTGCCAAACCATGTGAGACACAAGGGCGTGTGTCTGGT
Found at i:29245975 original size:41 final size:41
Alignment explanation
Indices: 29245904--29245987 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
29245894 TGAGCCATAA
* * **
29245904 GGGCGTGTGTCTGGTTGTGTGTCAGACCATGTGAGACACAC
1 GGGCGTGTGTCTAGCTGCATGTCAGACCATGTGAGACACAC
* *
29245945 GGGCGTGTGTCTAGCTGCATGTCTAG-CCATGTGGGCCACAC
1 GGGCGTGTGTCTAGCTGCATGTC-AGACCATGTGAGACACAC
29245986 GG
1 GG
29245988 TCTAGACAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
41 34 0.94
42 2 0.06
ACGTcount: A:0.15, C:0.23, G:0.37, T:0.25
Consensus pattern (41 bp):
GGGCGTGTGTCTAGCTGCATGTCAGACCATGTGAGACACAC
Found at i:29251121 original size:884 final size:884
Alignment explanation
Indices: 29249413--29251183 Score: 3542
Period size: 884 Copynumber: 2.0 Consensus size: 884
29249403 ATTTAAAATC
29249413 AGTAGCATACTTATCGAACACATGTAAGGTATGCCTTCTTAATTCAATTTCTAATGTTTCTACTT
1 AGTAGCATACTTATCGAACACATGTAAGGTATGCCTTCTTAATTCAATTTCTAATGTTTCTACTT
29249478 TTCTTGCCTTGTAGAACTTGTGGAGAATTATCAATGTTCAACATACCTCTCTCCCACAAGTAAAA
66 TTCTTGCCTTGTAGAACTTGTGGAGAATTATCAATGTTCAACATACCTCTCTCCCACAAGTAAAA
29249543 TTATCTATCGGTGGTAGAGTAATGTAATTGGAAGTCCATCAATGGATCCTTGAAATCTTGTAACA
131 TTATCTATCGGTGGTAGAGTAATGTAATTGGAAGTCCATCAATGGATCCTTGAAATCTTGTAACA
29249608 AGGAAACACCACTACACAGATTCGAATTATGGTTAGTTAAAACATAATCATTCCTTACTTTTTCA
196 AGGAAACACCACTACACAGATTCGAATTATGGTTAGTTAAAACATAATCATTCCTTACTTTTTCA
29249673 TGAATATTTTCTTGTTTTTCATTTTCTTTTCCCATTTGAGAACTCTCCAATTTTACCTCATATGT
261 TGAATATTTTCTTGTTTTTCATTTTCTTTTCCCATTTGAGAACTCTCCAATTTTACCTCATATGT
29249738 ATTTTCACTCACCAAAAGAGGACCATCAAGTAGATTTTTATCACTCAAGGTCTCTTTTCTCTCTA
326 ATTTTCACTCACCAAAAGAGGACCATCAAGTAGATTTTTATCACTCAAGGTCTCTTTTCTCTCTA
29249803 TCTTTTCAATTTTTTCTTCTTTACTTTCCTTTTCCCCCATACAAGTATTATGAATATTGAATTTA
391 TCTTTTCAATTTTTTCTTCTTTACTTTCCTTTTCCCCCATACAAGTATTATGAATATTGAATTTA
29249868 GTACAATACATCTCAGTAGAAGGACATGGCATTTCTATCTCATCTAACTCCATAAATTCAAGGAA
456 GTACAATACATCTCAGTAGAAGGACATGGCATTTCTATCTCATCTAACTCCATAAATTCAAGGAA
29249933 AAAAATTCCCACTATCATCTTTTTCCGGTTCACAATGTTCACTATCACAAATCTCTTTTCCGTTA
521 AAAAATTCCCACTATCATCTTTTTCCGGTTCACAATGTTCACTATCACAAATCTCTTTTCCGTTA
29249998 GAGTAAAAGTCAACAAAAGGTACAAAGTCATACTTACTTTCTTCTCTAGTTGGATATTTAATTGA
586 GAGTAAAAGTCAACAAAAGGTACAAAGTCATACTTACTTTCTTCTCTAGTTGGATATTTAATTGA
29250063 GCATTGAAAACCCTTATGATCCTTTGAGCTACACCAATAACATTGCACAAAAGGTGATAACTCAA
651 GCATTGAAAACCCTTATGATCCTTTGAGCTACACCAATAACATTGCACAAAAGGTGATAACTCAA
29250128 TCATATTCTCTCTATTTGGATATTTAATTAAACATCAAAAACCCTCATGATTTGTTGAACTACAC
716 TCATATTCTCTCTATTTGGATATTTAATTAAACATCAAAAACCCTCATGATTTGTTGAACTACAC
29250193 CAATAATATTTCACAACATGTGAGAGATCAGTTGTACTCCTTTCATTTGATCATCTCTCCTTGAA
781 CAATAATATTTCACAACATGTGAGAGATCAGTTGTACTCCTTTCATTTGATCATCTCTCCTTGAA
29250258 CTGACAAACTAATTTATGGTCACCTTTCCCATCATAGTA
846 CTGACAAACTAATTTATGGTCACCTTTCCCATCATAGTA
29250297 AGTAGCATACTTATCGAACACATGTAAGGTATGCCTTCTTAATTCAATTTCTAATGTTTCTACTT
1 AGTAGCATACTTATCGAACACATGTAAGGTATGCCTTCTTAATTCAATTTCTAATGTTTCTACTT
29250362 TTCTTGCCTTGTAGAACTTGTGGAGAATTATCAATGTTCAACATACCTCTCTCCCACAAGTAAAA
66 TTCTTGCCTTGTAGAACTTGTGGAGAATTATCAATGTTCAACATACCTCTCTCCCACAAGTAAAA
29250427 TTATCTATCGGTGGTAGAGTAATGTAATTGGAAGTCCATCAATGGATCCTTGAAATCTTGTAACA
131 TTATCTATCGGTGGTAGAGTAATGTAATTGGAAGTCCATCAATGGATCCTTGAAATCTTGTAACA
29250492 AGGAAACACCACTACACAGATTCGAATTATGGTTAGTTAAAACATAATCATTCCTTACTTTTTCA
196 AGGAAACACCACTACACAGATTCGAATTATGGTTAGTTAAAACATAATCATTCCTTACTTTTTCA
29250557 TGAATATTTTCTTGTTTTTCATTTTCTTTTCCCATTTGAGAACTCTCCAATTTTACCTCATATGT
261 TGAATATTTTCTTGTTTTTCATTTTCTTTTCCCATTTGAGAACTCTCCAATTTTACCTCATATGT
29250622 ATTTTCACTCACCAAAAGAGGACCATCAAGTAGATTTTTATCACTCAAGGTCTCTTTTCTCTCTA
326 ATTTTCACTCACCAAAAGAGGACCATCAAGTAGATTTTTATCACTCAAGGTCTCTTTTCTCTCTA
29250687 TCTTTTCAATTTTTTCTTCTTTACTTTCCTTTTCCCCCATACAAGTATTATGAATATTGAATTTA
391 TCTTTTCAATTTTTTCTTCTTTACTTTCCTTTTCCCCCATACAAGTATTATGAATATTGAATTTA
29250752 GTACAATACATCTCAGTAGAAGGACATGGCATTTCTATCTCATCTAACTCCATAAATTCAAGGAA
456 GTACAATACATCTCAGTAGAAGGACATGGCATTTCTATCTCATCTAACTCCATAAATTCAAGGAA
29250817 AAAAATTCCCACTATCATCTTTTTCCGGTTCACAATGTTCACTATCACAAATCTCTTTTCCGTTA
521 AAAAATTCCCACTATCATCTTTTTCCGGTTCACAATGTTCACTATCACAAATCTCTTTTCCGTTA
29250882 GAGTAAAAGTCAACAAAAGGTACAAAGTCATACTTACTTTCTTCTCTAGTTGGATATTTAATTGA
586 GAGTAAAAGTCAACAAAAGGTACAAAGTCATACTTACTTTCTTCTCTAGTTGGATATTTAATTGA
29250947 GCATTGAAAACCCTTATGATCCTTTGAGCTACACCAATAACATTGCACAAAAGGTGATAACTCAA
651 GCATTGAAAACCCTTATGATCCTTTGAGCTACACCAATAACATTGCACAAAAGGTGATAACTCAA
29251012 TCATATTCTCTCTATTTGGATATTTAATTAAACATCAAAAACCCTCATGATTTGTTGAACTACAC
716 TCATATTCTCTCTATTTGGATATTTAATTAAACATCAAAAACCCTCATGATTTGTTGAACTACAC
29251077 CAATAATATTTCACAACATGTGAGAGATCAGTTGTACTCCTTTCATTTGATCATCTCTCCTTGAA
781 CAATAATATTTCACAACATGTGAGAGATCAGTTGTACTCCTTTCATTTGATCATCTCTCCTTGAA
29251142 CTGACAAACTAATTTATGGTCACCTTTCCCATCATAGTA
846 CTGACAAACTAATTTATGGTCACCTTTCCCATCATAGTA
29251181 AGT
1 AGT
29251184 CTCTTGATCA
Statistics
Matches: 887, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
884 887 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (884 bp):
AGTAGCATACTTATCGAACACATGTAAGGTATGCCTTCTTAATTCAATTTCTAATGTTTCTACTT
TTCTTGCCTTGTAGAACTTGTGGAGAATTATCAATGTTCAACATACCTCTCTCCCACAAGTAAAA
TTATCTATCGGTGGTAGAGTAATGTAATTGGAAGTCCATCAATGGATCCTTGAAATCTTGTAACA
AGGAAACACCACTACACAGATTCGAATTATGGTTAGTTAAAACATAATCATTCCTTACTTTTTCA
TGAATATTTTCTTGTTTTTCATTTTCTTTTCCCATTTGAGAACTCTCCAATTTTACCTCATATGT
ATTTTCACTCACCAAAAGAGGACCATCAAGTAGATTTTTATCACTCAAGGTCTCTTTTCTCTCTA
TCTTTTCAATTTTTTCTTCTTTACTTTCCTTTTCCCCCATACAAGTATTATGAATATTGAATTTA
GTACAATACATCTCAGTAGAAGGACATGGCATTTCTATCTCATCTAACTCCATAAATTCAAGGAA
AAAAATTCCCACTATCATCTTTTTCCGGTTCACAATGTTCACTATCACAAATCTCTTTTCCGTTA
GAGTAAAAGTCAACAAAAGGTACAAAGTCATACTTACTTTCTTCTCTAGTTGGATATTTAATTGA
GCATTGAAAACCCTTATGATCCTTTGAGCTACACCAATAACATTGCACAAAAGGTGATAACTCAA
TCATATTCTCTCTATTTGGATATTTAATTAAACATCAAAAACCCTCATGATTTGTTGAACTACAC
CAATAATATTTCACAACATGTGAGAGATCAGTTGTACTCCTTTCATTTGATCATCTCTCCTTGAA
CTGACAAACTAATTTATGGTCACCTTTCCCATCATAGTA
Found at i:29254139 original size:27 final size:27
Alignment explanation
Indices: 29254100--29254152 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
29254090 CATGGTAGTT
*
29254100 AAAGAACTGCCTTTGTGGCGAACTCTA
1 AAAGAACTACCTTTGTGGCGAACTCTA
*
29254127 AAAGAACTACCTTTGTGGTGAACTCT
1 AAAGAACTACCTTTGTGGCGAACTCT
29254153 GAATGAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (27 bp):
AAAGAACTACCTTTGTGGCGAACTCTA
Found at i:29255903 original size:16 final size:17
Alignment explanation
Indices: 29255873--29255907 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29255863 TAATAATAAC
*
29255873 TCATCCAAGTAATTATT
1 TCATCCAACTAATTATT
29255890 TCATCCAACT-ATTATT
1 TCATCCAACTAATTATT
29255906 TC
1 TC
29255908 TCTCCCCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.43
Consensus pattern (17 bp):
TCATCCAACTAATTATT
Found at i:29257305 original size:15 final size:15
Alignment explanation
Indices: 29257281--29257310 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29257271 AACTTATAAT
*
29257281 GCTTAGTTTCAATGA
1 GCTTAATTTCAATGA
29257296 GCTTAATTTCAATGA
1 GCTTAATTTCAATGA
29257311 ATCCATTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (15 bp):
GCTTAATTTCAATGA
Found at i:29263333 original size:44 final size:44
Alignment explanation
Indices: 29263265--29263396 Score: 210
Period size: 44 Copynumber: 3.0 Consensus size: 44
29263255 CCTCATTAAT
*
29263265 ATTAGCTCTTCTAGAGTTTTCAACTAATTTTGTACTACCAAATA
1 ATTAGCTCTTCTAGAGCTTTCAACTAATTTTGTACTACCAAATA
* * * *
29263309 ATTAACTCTTCTAGAGCTTTCAACTAATTTTATGCTGCCAAATA
1 ATTAGCTCTTCTAGAGCTTTCAACTAATTTTGTACTACCAAATA
*
29263353 ATTAGCTCTTCTAGAGCTTTCAACTAATTTTGAACTACCAAATA
1 ATTAGCTCTTCTAGAGCTTTCAACTAATTTTGTACTACCAAATA
29263397 TTACATTAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 78 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (44 bp):
ATTAGCTCTTCTAGAGCTTTCAACTAATTTTGTACTACCAAATA
Found at i:29264230 original size:2 final size:2
Alignment explanation
Indices: 29264223--29264276 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
29264213 AAATTGAGAG
29264223 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29264265 CT CT CT CT CT CT
1 CT CT CT CT CT CT
29264277 TTTGCTTGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29273482 original size:27 final size:28
Alignment explanation
Indices: 29273452--29273554 Score: 117
Period size: 27 Copynumber: 3.7 Consensus size: 28
29273442 TATTTCATTA
* *
29273452 AAATTATTAAAATTTATAAAAA-CTTAT
1 AAATTATTAAAATATATAAAAATCTAAT
29273479 AAA-TATTAAAAATATATAAAAATCTAAT
1 AAATTATT-AAAATATATAAAAATCTAAT
29273507 AAATTA-TAAAATATAT-AAAAT-TAAT
1 AAATTATTAAAATATATAAAAATCTAAT
29273532 AAAACTTATTTAAAATATATAAA
1 -AAA-TTA-TTAAAATATATAAA
29273555 TTTAAAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 13
0.81 0.02 0.16
Matches are distributed among these distances:
25 4 0.06
26 12 0.18
27 28 0.42
28 8 0.12
29 12 0.18
30 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATTATTAAAATATATAAAAATCTAAT
Found at i:29273508 original size:11 final size:10
Alignment explanation
Indices: 29273451--29273554 Score: 57
Period size: 10 Copynumber: 11.2 Consensus size: 10
29273441 TTATTTCATT
*
29273451 AAAAT-TATT
1 AAAATATATA
*
29273460 AAAATTTATA
1 AAAATATATA
29273470 AAAACT-TAT-
1 AAAA-TATATA
29273479 -AAATAT-TA
1 AAAATATATA
29273487 AAAATATATA
1 AAAATATATA
*
29273497 AAAATCTA-A
1 AAAATATATA
*
29273506 TAAAT-TAT-
1 AAAATATATA
29273514 AAAATATATA
1 AAAATATATA
*
29273524 AAATTA-ATA
1 AAAATATATA
* *
29273533 AAACT-TATTT
1 AAAATATA-TA
29273543 AAAATATATA
1 AAAATATATA
29273553 AA
1 AA
29273555 TTTAAAAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
7 2 0.03
8 10 0.14
9 27 0.36
10 32 0.43
11 3 0.04
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATATATA
Found at i:29273545 original size:29 final size:28
Alignment explanation
Indices: 29273450--29273564 Score: 100
Period size: 27 Copynumber: 4.2 Consensus size: 28
29273440 ATTATTTCAT
*
29273450 TAAAATTA-TTAAAATTTATAAAAACTT-A
1 TAAAATTATTTAAAATATAT-AAAA-TTAA
*
29273478 T-AAA-TATTAAAAATATATAAAAATCTAA
1 TAAAATTATTTAAAATATAT-AAAAT-TAA
29273506 T-AAATTA--TAAAATATATAAAATTAA
1 TAAAATTATTTAAAATATATAAAATTAA
*
29273531 TAAAACTTATTTAAAATATATAAATTTAA
1 TAAAA-TTATTTAAAATATATAAAATTAA
*
29273560 AAAAA
1 TAAAA
29273565 AATAAAATTC
Statistics
Matches: 74, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
25 4 0.05
26 11 0.15
27 30 0.41
28 6 0.08
29 23 0.31
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAAATTATTTAAAATATATAAAATTAA
Found at i:29273554 original size:9 final size:9
Alignment explanation
Indices: 29273450--29273554 Score: 53
Period size: 9 Copynumber: 11.4 Consensus size: 9
29273440 ATTATTTCAT
29273450 TAAAAT-TA
1 TAAAATATA
*
29273458 TTAAAATTTA
1 -TAAAATATA
29273468 TAAAA-ACT-
1 TAAAATA-TA
29273476 TATAAATAT-
1 TA-AAATATA
29273485 TAAAAATATA
1 T-AAAATATA
*
29273495 TAAAA-ATC
1 TAAAATATA
29273503 TAATAA-ATTA
1 TAA-AATA-TA
29273513 TAAAATATA
1 TAAAATATA
29273522 TAAAAT-TAA
1 TAAAATAT-A
*
29273531 TAAAACTTATT
1 TAAAA--TATA
29273542 TAAAATATA
1 TAAAATATA
29273551 TAAA
1 TAAA
29273555 TTTAAAAAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 26
0.72 0.05 0.24
Matches are distributed among these distances:
8 8 0.10
9 53 0.68
10 10 0.13
11 6 0.08
12 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAATATA
Found at i:29273594 original size:21 final size:21
Alignment explanation
Indices: 29273568--29273612 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29273558 AAAAAAAAAT
*
29273568 AAAATTCTTAAAAACTAATAA
1 AAAATTCTAAAAAACTAATAA
* * *
29273589 AAAATTGTAAAAAAGTATTAA
1 AAAATTCTAAAAAACTAATAA
29273610 AAA
1 AAA
29273613 TATTAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAATTCTAAAAAACTAATAA
Found at i:29273656 original size:19 final size:19
Alignment explanation
Indices: 29273451--29273656 Score: 69
Period size: 19 Copynumber: 11.1 Consensus size: 19
29273441 TTATTTCATT
*
29273451 AAAATTAT-TAAAATTTATA
1 AAAATTATATAAAA-ATATA
* *
29273470 AAAACT-TATAAATAT-TA
1 AAAATTATATAAAAATATA
*
29273487 AAAA-TATATAAAAATCTA
1 AAAATTATATAAAAATATA
*
29273505 ATAAATTATA-AAATATAT-
1 A-AAATTATATAAAAATATA
* *
29273523 AAAATTA-ATAAAACTTATTT
1 AAAATTATATAAAA-ATA-TA
*
29273543 AAAA-TATAT--AAATTTA
1 AAAATTATATAAAAATATA
* * * *
29273559 AAAA-AAAATAAAATTCTTA
1 AAAATTATATAAAAAT-ATA
* *
29273578 AAAACTA-ATAAAAAATTGTAA
1 AAAATTATAT-AAAAA-TAT-A
* *
29273599 AAAAGTAT-TAAAAATATT
1 AAAATTATATAAAAATATA
**
29273617 AAAATTGATATAAACTTATA
1 AAAATT-ATATAAAAATATA
*
29273637 AAAATTATATAAAAAAATA
1 AAAATTATATAAAAATATA
29273656 A
1 A
29273657 TACAAACTTG
Statistics
Matches: 140, Mismatches: 27, Indels: 40
0.68 0.13 0.19
Matches are distributed among these distances:
16 10 0.07
17 24 0.17
18 18 0.13
19 45 0.32
20 34 0.24
21 9 0.06
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (19 bp):
AAAATTATATAAAAATATA
Found at i:29274045 original size:9 final size:9
Alignment explanation
Indices: 29274017--29274274 Score: 94
Period size: 9 Copynumber: 27.1 Consensus size: 9
29274007 TCTGGCCTAG
*
29274017 TTTTTATGA
1 TTTTTATAA
29274026 TTTTCTAATAA
1 TTTT-T-ATAA
*
29274037 CTTTTATAA
1 TTTTTATAA
* *
29274046 GTTTATATCAG
1 -TTTTTAT-AA
* *
29274057 TTTTAATAT
1 TTTTTATAA
29274066 TTTTTATAA
1 TTTTTATAA
*
29274075 TTTTTATTA
1 TTTTTATAA
29274084 TTTTTATAGAA
1 TTTTTAT--AA
* *
29274095 TTTTAATATG
1 TTTTTATA-A
29274105 TTTTTATAAA
1 TTTTTAT-AA
* *
29274115 ATTTTAAACA
1 TTTTTATA-A
*
29274125 TTTTAACT-A
1 TTTTTA-TAA
29274134 TGTTTTATCAA
1 T-TTTTAT-AA
29274145 -TTTTATAA
1 TTTTTATAA
29274153 TTTTTTTATAA
1 --TTTTTATAA
*
29274164 TTTATTAGAA
1 TTT-TTATAA
29274174 TTTTTAT-A
1 TTTTTATAA
29274182 TTTTTATAA
1 TTTTTATAA
* *
29274191 TATTTACAA
1 TTTTTATAA
29274200 TTTTTTATAA
1 -TTTTTATAA
**
29274210 GTTCATATAGA
1 -TTTTTATA-A
*
29274221 TTTTTATAT
1 TTTTTATAA
*
29274230 TTTTTAAAA
1 TTTTTATAA
*
29274239 TATTTAATAA
1 T-TTTTATAA
* *
29274249 -ATTTAT-T
1 TTTTTATAA
* *
29274256 TTTTTGTGA
1 TTTTTATAA
29274265 TTTTTATAA
1 TTTTTATAA
29274274 T
1 T
29274275 AATTTTAATG
Statistics
Matches: 180, Mismatches: 46, Indels: 46
0.66 0.17 0.17
Matches are distributed among these distances:
8 18 0.10
9 72 0.40
10 65 0.36
11 25 0.14
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29274079 original size:19 final size:19
Alignment explanation
Indices: 29274057--29274121 Score: 78
Period size: 19 Copynumber: 3.3 Consensus size: 19
29274047 TTTATATCAG
*
29274057 TTTTAATATTTTTTATAAT
1 TTTTAATATTTTTTATAAA
*
29274076 TTTTATTA-TTTTTATAGAA
1 TTTTAATATTTTTTATA-AA
29274095 TTTTAATATGTTTTTATAAAA
1 TTTTAATAT-TTTTTAT-AAA
29274116 TTTTAA
1 TTTTAA
29274122 ACATTTTAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 8 0.21
19 15 0.38
21 15 0.38
22 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTAATATTTTTTATAAA
Found at i:29274177 original size:19 final size:18
Alignment explanation
Indices: 29274155--29274204 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
29274145 TTTTATAATT
29274155 TTTTTATAATTTATTAGAA
1 TTTTTATAATTT-TTAGAA
*
29274174 TTTTTAT-ATTTTTATAA
1 TTTTTATAATTTTTAGAA
* *
29274191 TATTTACAATTTTT
1 TTTTTATAATTTTT
29274205 TATAAGTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 10 0.37
18 10 0.37
19 7 0.26
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATAATTTTTAGAA
Found at i:29274241 original size:48 final size:46
Alignment explanation
Indices: 29274154--29274244 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 46
29274144 ATTTTATAAT
* *
29274154 TTTTTTATAATTTATTAGAATTTTTATATTTTTATAATATTTACAA
1 TTTTTTATAATTCATTAGAATTTTTATATTTTTAAAATATTTACAA
29274200 TTTTTTATAAGTTCATATAG-ATTTTTATATTTTTTAAAATATTTA
1 TTTTTTATAA-TTCAT-TAGAATTTTTATA-TTTTTAAAATATTTA
29274245 ATAAATTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
46 10 0.25
47 13 0.32
48 17 0.43
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (46 bp):
TTTTTTATAATTCATTAGAATTTTTATATTTTTAAAATATTTACAA
Found at i:29282395 original size:16 final size:18
Alignment explanation
Indices: 29282369--29282405 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
29282359 GTCATTGTGG
29282369 AAATAATAGCACAT-ATC
1 AAATAATAGCACATAATC
*
29282386 AAAT-ATAGCATATAATC
1 AAATAATAGCACATAATC
29282403 AAA
1 AAA
29282406 CTCAACTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAATAGCACATAATC
Found at i:29285818 original size:29 final size:28
Alignment explanation
Indices: 29285769--29285835 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 28
29285759 GATGGAGAAG
29285769 AAGTATAAACATATTGAGCCATTTACGCAAA
1 AAGTA-AAA-ATATTGAGCCATTTACG-AAA
*
29285800 AAGTAAAAATATT-AGGCCATTTATGAAA
1 AAGTAAAAATATTGA-GCCATTTACGAAA
29285828 AA-TAAAAA
1 AAGTAAAAA
29285836 AAAGGACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 6 0.18
28 6 0.18
29 14 0.41
30 3 0.09
31 5 0.15
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.25
Consensus pattern (28 bp):
AAGTAAAAATATTGAGCCATTTACGAAA
Found at i:29286000 original size:31 final size:31
Alignment explanation
Indices: 29285962--29286040 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
29285952 TTAATGAGTG
29285962 ACTGATTTGTTACTTTTCGATAACATTAGAA
1 ACTGATTTGTTACTTTTCGATAACATTAGAA
* * **
29285993 ACTGATTTGTCACTTTTCGATAACGTTAGTG
1 ACTGATTTGTTACTTTTCGATAACATTAGAA
*
29286024 ACTGATTTGTTATTTTT
1 ACTGATTTGTTACTTTT
29286041 TTAAAGTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (31 bp):
ACTGATTTGTTACTTTTCGATAACATTAGAA
Found at i:29297171 original size:83 final size:82
Alignment explanation
Indices: 29297019--29297247 Score: 251
Period size: 83 Copynumber: 2.7 Consensus size: 82
29297009 TACACCTGTT
* * * * * * * ***
29297019 CTTTTTGACACAATACTTAAAACTACTCATAACCCTTCTCTAACCGATAAATAATAAGATAATGT
1 CTTTTT-ACACAATGCTTAGAACTACTCAT-TCCCCTCCCCAACCGATAAATAGTAAGATAACAC
*
29297084 GCTTCAGCGCACTCAAACC
64 GCTTCAGCACACTCAAACC
29297103 CTTTTTACACAATGCTTAGAACTACTCATTCTCCCTCCCCAACCGATAAATAGTAAGATAACACG
1 CTTTTTACACAATGCTTAGAACTACTCATTC-CCCTCCCCAACCGATAAATAGTAAGATAACACG
*
29297168 CTTCAGCACACTCGAACC
65 CTTCAGCACACTCAAACC
* * * ** *
29297186 CTTTTTTACAAAATGCTTCGAACTACTCGTTACCCCTCCCCAACTAATAAATAGTAACATAA
1 C-TTTTTACACAATGCTTAGAACTACTCATT-CCCCTCCCCAACCGATAAATAGTAAGATAA
29297248 TATGTTTCAG
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
82 1 0.01
83 64 0.52
84 58 0.47
85 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.28
Consensus pattern (82 bp):
CTTTTTACACAATGCTTAGAACTACTCATTCCCCTCCCCAACCGATAAATAGTAAGATAACACGC
TTCAGCACACTCAAACC
Found at i:29297257 original size:84 final size:83
Alignment explanation
Indices: 29297060--29297258 Score: 247
Period size: 84 Copynumber: 2.4 Consensus size: 83
29297050 ACCCTTCTCT
* * * * *
29297060 AACCGATAAATAATAAGATAATGTGCTTCAGCGCACTCAAACCCTTTTTACACAATGCTTAGAAC
1 AACCAATAAATAGTAAGATAATATGCTTCAGCACACTCAAACCCTTTTTACAAAATGCTTAGAAC
29297125 TACTCATTCTCCCTCCCC
66 TACTCATTCTCCCTCCCC
* * * * *
29297143 AACCGATAAATAGTAAGATAACACGCTTCAGCACACTCGAACCCTTTTTTACAAAATGCTTCGAA
1 AACCAATAAATAGTAAGATAATATGCTTCAGCACACTCAAACCC-TTTTTACAAAATGCTTAGAA
*
29297208 CTACTCGTTAC-CCCTCCCC
65 CTACTCATT-CTCCCTCCCC
* * *
29297227 AACTAATAAATAGTAACATAATATGTTTCAGC
1 AACCAATAAATAGTAAGATAATATGCTTCAGC
29297259 GTTTCAGCGC
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
83 38 0.38
84 60 0.61
85 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.27
Consensus pattern (83 bp):
AACCAATAAATAGTAAGATAATATGCTTCAGCACACTCAAACCCTTTTTACAAAATGCTTAGAAC
TACTCATTCTCCCTCCCC
Found at i:29298453 original size:19 final size:19
Alignment explanation
Indices: 29298426--29298470 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
29298416 ATTAATTAAC
29298426 TTTTT-ATAATTTTATAT-A
1 TTTTTAATAATTTTA-ATGA
29298444 TTTTTAATAATTTTAATGA
1 TTTTTAATAATTTTAATGA
29298463 TTTTTAAT
1 TTTTTAAT
29298471 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTAATAATTTTAATGA
Found at i:29298475 original size:9 final size:9
Alignment explanation
Indices: 29298426--29298477 Score: 54
Period size: 10 Copynumber: 5.8 Consensus size: 9
29298416 ATTAATTAAC
29298426 TTTTT-ATA
1 TTTTTAATA
*
29298434 ATTTTATATA
1 TTTTTA-ATA
29298444 TTTTTAATA
1 TTTTTAATA
*
29298453 ATTTTAATGA
1 TTTTTAAT-A
29298463 TTTTTAAT-
1 TTTTTAATA
29298471 TTTTTAA
1 TTTTTAA
29298478 AAATTAATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 11 0.30
9 10 0.27
10 16 0.43
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTAATA
Found at i:29298874 original size:29 final size:28
Alignment explanation
Indices: 29298842--29299006 Score: 89
Period size: 29 Copynumber: 5.6 Consensus size: 28
29298832 CGTTTTTTTA
29298842 GTCACCCAACTATCAATTCTTTTAATTTG
1 GTCACCCAACTATCAATT-TTTTAATTTG
*** * *
29298871 GTCATTTAACTATTGCAATTTTCTT-TTTTA
1 GTCACCCAACTA-T-CAATTTT-TTAATTTG
* * *
29298901 ATCACTCAACTATCAGTTCTTTTAATTTG
1 GTCACCCAACTATCAATT-TTTTAATTTG
** ** *
29298930 GTCACCCAACTATTGCTCTTTTTCTTTTTTT
1 GTCACCCAACTA-T-CAATTTTT-TAATTTG
* *
29298961 GTCACCTAACTATCATTTTTTTTAATTTG
1 GTCACCCAACTATCA-ATTTTTTAATTTG
*
29298990 ATCACCCAACTAATCAA
1 GTCACCCAACT-ATCAA
29299007 AATTGTTTTT
Statistics
Matches: 99, Mismatches: 27, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
28 6 0.06
29 39 0.39
30 29 0.29
31 25 0.25
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (28 bp):
GTCACCCAACTATCAATTTTTTAATTTG
Found at i:29298912 original size:59 final size:59
Alignment explanation
Indices: 29298835--29299001 Score: 201
Period size: 59 Copynumber: 2.8 Consensus size: 59
29298825 TTGTTCCCGT
***
29298835 TTTTTTAGTCACCCAACTATCAATTCTTTTAATTTGGTCATTTAACTATTGC-AATTTTC
1 TTTTTTAGTCA-CCAACTATCAATTCTTTTAATTTGGTCACCCAACTATTGCTAATTTTC
* * **
29298894 TTTTTTAATCACTCAACTATCAGTTCTTTTAATTTGGTCACCCAACTATTGCTCTTTTTC
1 TTTTTTAGTCAC-CAACTATCAATTCTTTTAATTTGGTCACCCAACTATTGCTAATTTTC
* * * *
29298954 TTTTTTTGTCACCTAACTATCATTTTTTTTAATTTGATCACCCAACTA
1 TTTTTTAGTCACC-AACTATCAATTCTTTTAATTTGGTCACCCAACTA
29299002 ATCAAAATTG
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
58 1 0.01
59 46 0.49
60 46 0.49
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (59 bp):
TTTTTTAGTCACCAACTATCAATTCTTTTAATTTGGTCACCCAACTATTGCTAATTTTC
Found at i:29298984 original size:60 final size:59
Alignment explanation
Indices: 29298834--29299001 Score: 194
Period size: 60 Copynumber: 2.8 Consensus size: 59
29298824 ATTGTTCCCG
* ***
29298834 TTTTTTTAGTCACCCAACTATCAATTCTTTTAATTTGGTCATTTAACTATTGCAATTTTC
1 TTTTTTT-GTCACCTAACTATCAATTCTTTTAATTTGGTCACCCAACTATTGCAATTTTC
** * **
29298894 TTTTTTAATCA-CTCAACTATCAGTTCTTTTAATTTGGTCACCCAACTATTGCTCTTTTTC
1 TTTTTTTGTCACCT-AACTATCAATTCTTTTAATTTGGTCACCCAACTATTGC-AATTTTC
* * *
29298954 TTTTTTTGTCACCTAACTATCATTTTTTTTAATTTGATCACCCAACTA
1 TTTTTTTGTCACCTAACTATCAATTCTTTTAATTTGGTCACCCAACTA
29299002 ATCAAAATTG
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
58 1 0.01
59 37 0.41
60 51 0.56
61 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (59 bp):
TTTTTTTGTCACCTAACTATCAATTCTTTTAATTTGGTCACCCAACTATTGCAATTTTC
Found at i:29311595 original size:44 final size:44
Alignment explanation
Indices: 29311532--29311619 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
29311522 ATGCCAAGGC
29311532 ACGAGCAACAACCCGGGGTGACAAGCTTGTGTATCCATTCTTAG
1 ACGAGCAACAACCCGGGGTGACAAGCTTGTGTATCCATTCTTAG
29311576 ACGAGCAACAACCCGGGGTGACAAGCTTGTGTATCCATTCTTAG
1 ACGAGCAACAACCCGGGGTGACAAGCTTGTGTATCCATTCTTAG
29311620 TCTGTGTCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (44 bp):
ACGAGCAACAACCCGGGGTGACAAGCTTGTGTATCCATTCTTAG
Found at i:29313532 original size:14 final size:14
Alignment explanation
Indices: 29313515--29313712 Score: 148
Period size: 14 Copynumber: 14.1 Consensus size: 14
29313505 ATAAACCTGT
*
29313515 ATCTATGAATCCAC
1 ATCTATGAATCTAC
*
29313529 ATCTATGAATCTAT
1 ATCTATGAATCTAC
*
29313543 ATCTATGAATCTGC
1 ATCTATGAATCTAC
*
29313557 ATCTATGAATCCAC
1 ATCTATGAATCTAC
***
29313571 ATCTATGAATCCGT
1 ATCTATGAATCTAC
* * *
29313585 ATATAAGAATCTGC
1 ATCTATGAATCTAC
**
29313599 ATCTATGAATCTGT
1 ATCTATGAATCTAC
29313613 ATCTATGAATCTAC
1 ATCTATGAATCTAC
** *
29313627 ATGGATAAATCTAC
1 ATCTATGAATCTAC
*
29313641 ATCTATGAATCCAC
1 ATCTATGAATCTAC
* * *
29313655 ATGTATGGAT-TCGC
1 ATCTATGAATCT-AC
*
29313669 ATCTATGAATCTGC
1 ATCTATGAATCTAC
* *
29313683 ATGTATAGATTC-AC
1 ATCTAT-GAATCTAC
* *
29313697 ATTTATAAATCTAC
1 ATCTATGAATCTAC
29313711 AT
1 AT
29313713 GTAAGAGTCT
Statistics
Matches: 144, Mismatches: 36, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
13 3 0.02
14 136 0.94
15 5 0.03
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (14 bp):
ATCTATGAATCTAC
Found at i:29313680 original size:42 final size:42
Alignment explanation
Indices: 29313501--29313712 Score: 185
Period size: 42 Copynumber: 5.0 Consensus size: 42
29313491 GACATTCTGT
* * * *
29313501 ATCTATAAACCTGTATCTATGAATCCACATCTATGAATCTAT
1 ATCTATGAATCTGCATCTATGAATCCACATCTATGAATCTAC
***
29313543 ATCTATGAATCTGCATCTATGAATCCACATCTATGAATCCGT
1 ATCTATGAATCTGCATCTATGAATCCACATCTATGAATCTAC
* * ***
29313585 ATATAAGAATCTGCATCTATGAATCTGTATCTATGAATCTAC
1 ATCTATGAATCTGCATCTATGAATCCACATCTATGAATCTAC
** * * * * *
29313627 ATGGATAAATCTACATCTATGAATCCACATGTATGGAT-TCGC
1 ATCTATGAATCTGCATCTATGAATCCACATCTATGAATCT-AC
* * * *
29313669 ATCTATGAATCTGCATGTAT-AGATTCACATTTATAAATCTAC
1 ATCTATGAATCTGCATCTATGA-ATCCACATCTATGAATCTAC
29313711 AT
1 AT
29313713 GTAAGAGTCT
Statistics
Matches: 133, Mismatches: 34, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
41 2 0.02
42 130 0.98
43 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.35
Consensus pattern (42 bp):
ATCTATGAATCTGCATCTATGAATCCACATCTATGAATCTAC
Found at i:29325413 original size:43 final size:43
Alignment explanation
Indices: 29325258--29325414 Score: 135
Period size: 43 Copynumber: 3.7 Consensus size: 43
29325248 TGTGTTATCG
* *
29325258 TGTAAGACCACGTCTGGGACGTTGTCATCGAT-TTGAGATTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTA-A-TTACA
* * * * * *
29325302 TGTAAGACCATGTCTGGGACATTAGCGTCG-TATATT-ATTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATAT-TTAATTACA
* *
29325344 TGTAAGACC-CTGTTTGGAACAG-TGGCATCGATATTTAATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTAATTACA
*
29325387 TGGAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
29325415 TGCACGAGCT
Statistics
Matches: 86, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
42 28 0.33
43 30 0.35
44 27 0.31
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTAATTACA
Found at i:29327500 original size:20 final size:20
Alignment explanation
Indices: 29327477--29327580 Score: 73
Period size: 20 Copynumber: 5.2 Consensus size: 20
29327467 AGTACTAGCA
29327477 GCTTGTCTGCAATACTGGTG
1 GCTTGTCTGCAATACTGGTG
*** **
29327497 GCTTGTCCATAATACTGGCA
1 GCTTGTCTGCAATACTGGTG
* * *
29327517 GTTTGTCTGTAATACTAGTG
1 GCTTGTCTGCAATACTGGTG
* * * **
29327537 GCTTATCTACAATACTAGCA
1 GCTTGTCTGCAATACTGGTG
* *
29327557 GTTTATCTGCAATACTGGTG
1 GCTTGTCTGCAATACTGGTG
29327577 GCTT
1 GCTT
29327581 ATCCACAAAT
Statistics
Matches: 61, Mismatches: 23, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
GCTTGTCTGCAATACTGGTG
Found at i:29327538 original size:40 final size:40
Alignment explanation
Indices: 29327469--29327588 Score: 168
Period size: 40 Copynumber: 3.0 Consensus size: 40
29327459 AAGGAGGAAG
* * *
29327469 TACTAGCAGCTTGTCTGCAATACTGGTGGCTTGTCCATAA
1 TACTAGCAGTTTGTCTGCAATACTGGTGGCTTATCCACAA
* * * *
29327509 TACTGGCAGTTTGTCTGTAATACTAGTGGCTTATCTACAA
1 TACTAGCAGTTTGTCTGCAATACTGGTGGCTTATCCACAA
*
29327549 TACTAGCAGTTTATCTGCAATACTGGTGGCTTATCCACAA
1 TACTAGCAGTTTGTCTGCAATACTGGTGGCTTATCCACAA
29327589 ATTGGTATGT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (40 bp):
TACTAGCAGTTTGTCTGCAATACTGGTGGCTTATCCACAA
Found at i:29332042 original size:26 final size:26
Alignment explanation
Indices: 29332006--29332058 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
29331996 TAGTCCTAAG
29332006 TCCGTTTAGTCAAACAAGGGTTTTAA
1 TCCGTTTAGTCAAACAAGGGTTTTAA
29332032 TCCGTTTAGTCAAACAAGGGTTTTAA
1 TCCGTTTAGTCAAACAAGGGTTTTAA
29332058 T
1 T
29332059 AAGAAATTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (26 bp):
TCCGTTTAGTCAAACAAGGGTTTTAA
Found at i:29332174 original size:28 final size:28
Alignment explanation
Indices: 29332142--29332205 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
29332132 ATGGTTGATG
29332142 AATTTTTTGAA-GCAAAGAGAGTT-GCAGA
1 AATTTTTTGAACG-AAAGAGAGTTCGC-GA
* *
29332170 AATTTTTTGAACGAAATAGGGTTCGCGA
1 AATTTTTTGAACGAAAGAGAGTTCGCGA
29332198 AATTTTTT
1 AATTTTTT
29332206 AAGGATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (28 bp):
AATTTTTTGAACGAAAGAGAGTTCGCGA
Found at i:29333022 original size:11 final size:11
Alignment explanation
Indices: 29333006--29333039 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
29332996 GCTATGTGTA
29333006 TATATAATTTT
1 TATATAATTTT
*
29333017 TATATATTTTT
1 TATATAATTTT
29333028 TA-ATAATTTT
1 TATATAATTTT
29333038 TA
1 TA
29333040 AAAATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATAATTTT
Found at i:29336962 original size:59 final size:59
Alignment explanation
Indices: 29336849--29336974 Score: 141
Period size: 59 Copynumber: 2.1 Consensus size: 59
29336839 TCATTTTTTA
* **
29336849 GAATTTTTAGTATTAGAACTAAACTAACAAATTTTGTAATGTTGATGACCAAATTTATT
1 GAATTTTTAGAATTAGAACTAAACTAACAAATTTTGTAACATTGATGACCAAATTTATT
* * * *
29336908 GCATTTTTAGAATTAGAACTAATA-TGAC-AATTTTGTAAACATTGATGGA-TAAATTTGTT
1 GAATTTTTAGAATTAGAACTAA-ACTAACAAATTTTGT-AACATTGAT-GACCAAATTTATT
29336967 GAATTTTT
1 GAATTTTT
29336975 TAGCTATAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
58 8 0.14
59 45 0.80
60 3 0.05
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.42
Consensus pattern (59 bp):
GAATTTTTAGAATTAGAACTAAACTAACAAATTTTGTAACATTGATGACCAAATTTATT
Found at i:29342111 original size:26 final size:25
Alignment explanation
Indices: 29342073--29342123 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
29342063 AAAATGTTTT
* *
29342073 TTTTTGCAAAAATAATATTATATTA
1 TTTTTGAAAAAATAATATGATATTA
*
29342098 TTTTTGAAAGAAATATTATGATATTA
1 TTTTTGAAA-AAATAATATGATATTA
29342124 AACTATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTTGAAAAAATAATATGATATTA
Found at i:29351429 original size:23 final size:22
Alignment explanation
Indices: 29351403--29351445 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
29351393 TGTTATTAAT
29351403 ATTTATATTTATTATTTTTTGTA
1 ATTTATATTT-TTATTTTTTGTA
*
29351426 ATTTTTATTTTTATTTTTTG
1 ATTTATATTTTTATTTTTTG
29351446 AGTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (22 bp):
ATTTATATTTTTATTTTTTGTA
Found at i:29355710 original size:45 final size:45
Alignment explanation
Indices: 29355643--29355729 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
29355633 ATGATGTTAC
* * * * *
29355643 GTATTTAATATATTTTTGAAAAATGGAATGTTGTTAAATTATTAT
1 GTATTTAACATATTGTTAAAAAATGAAATATTGTTAAATTATTAT
*
29355688 GTATTTAGCATATTGTTAAAAAATGAAATATTGTTAAATTAT
1 GTATTTAACATATTGTTAAAAAATGAAATATTGTTAAATTAT
29355730 GAATTGAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.46
Consensus pattern (45 bp):
GTATTTAACATATTGTTAAAAAATGAAATATTGTTAAATTATTAT
Found at i:29355822 original size:24 final size:24
Alignment explanation
Indices: 29355790--29355835 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
29355780 GTTCTGTGGT
*
29355790 AAAGGATGAATTGACGACAAATGC
1 AAAGGATGAACTGACGACAAATGC
*
29355814 AAAGGATGAACTGACGGCAAAT
1 AAAGGATGAACTGACGACAAAT
29355836 TATCCAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.13, G:0.26, T:0.15
Consensus pattern (24 bp):
AAAGGATGAACTGACGACAAATGC
Found at i:29355997 original size:21 final size:21
Alignment explanation
Indices: 29355920--29356070 Score: 79
Period size: 21 Copynumber: 7.2 Consensus size: 21
29355910 TATTAACTCA
*
29355920 TATGAGTTTTAGTTTAACCCT
1 TATGAGTTTCAGTTTAACCCT
* * * * *
29355941 TATGGGTTTCCGTTCAGCTCT
1 TATGAGTTTCAGTTTAACCCT
* * *
29355962 TTTAAGTTTTAGTTTAACCCT
1 TATGAGTTTCAGTTTAACCCT
* * **
29355983 TATGAGTTTCCGTTTAGCTTT
1 TATGAGTTTCAGTTTAACCCT
* * *
29356004 TTTGAGCTTCAATTTAACCCT
1 TATGAGTTTCAGTTTAACCCT
* ** * *
29356025 TATGGGTTTTTGTTTAGCTCT
1 TATGAGTTTCAGTTTAACCCT
* *
29356046 TACGAGCTTCCA-TTTAACCCT
1 TATGAG-TTTCAGTTTAACCCT
29356067 TATG
1 TATG
29356071 GGGTTCTGCT
Statistics
Matches: 85, Mismatches: 44, Indels: 2
0.65 0.34 0.02
Matches are distributed among these distances:
21 83 0.98
22 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (21 bp):
TATGAGTTTCAGTTTAACCCT
Found at i:29356040 original size:42 final size:42
Alignment explanation
Indices: 29355932--29356072 Score: 174
Period size: 42 Copynumber: 3.4 Consensus size: 42
29355922 TGAGTTTTAG
* * * * *
29355932 TTTAACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGTTTTAG
1 TTTAACCCTTATGGGTTTCCGTTTAGCTCTTTTGAGCTTCAA
* *
29355974 TTTAACCCTTATGAGTTTCCGTTTAGCTTTTTTGAGCTTCAA
1 TTTAACCCTTATGGGTTTCCGTTTAGCTCTTTTGAGCTTCAA
** ** *
29356016 TTTAACCCTTATGGGTTTTTGTTTAGCTCTTACGAGCTTCCA
1 TTTAACCCTTATGGGTTTCCGTTTAGCTCTTTTGAGCTTCAA
29356058 TTTAACCCTTATGGG
1 TTTAACCCTTATGGG
29356073 GTTCTGCTTA
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.46
Consensus pattern (42 bp):
TTTAACCCTTATGGGTTTCCGTTTAGCTCTTTTGAGCTTCAA
Found at i:29356097 original size:42 final size:42
Alignment explanation
Indices: 29356007--29356089 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
29355997 TAGCTTTTTT
* * * *
29356007 GAGCTTCAATTTAACCCTTATGGGTTTTTGTTTAGCTCTTAC
1 GAGCTTCAATTTAACCCTTATGGGGTTCTGCTTAGCACTTAC
* *
29356049 GAGCTTCCATTTAACCCTTATGGGGTTCTGCTTATCACTTA
1 GAGCTTCAATTTAACCCTTATGGGGTTCTGCTTAGCACTTA
29356090 TGTGCTTCTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (42 bp):
GAGCTTCAATTTAACCCTTATGGGGTTCTGCTTAGCACTTAC
Found at i:29359117 original size:20 final size:19
Alignment explanation
Indices: 29359089--29359138 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
29359079 CCACTCTCAA
29359089 TCTCTTTTTTCTCTTTTTCAT
1 TCTC-TTTTTCT-TTTTTCAT
*
29359110 TCTCTTTTTCTTTTTTGAT
1 TCTCTTTTTCTTTTTTCAT
29359129 T-TCTTTTTCT
1 TCTCTTTTTCT
29359139 GTCTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 7 0.25
21 4 0.14
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (19 bp):
TCTCTTTTTCTTTTTTCAT
Found at i:29359123 original size:18 final size:17
Alignment explanation
Indices: 29359095--29359138 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
29359085 TCAATCTCTT
29359095 TTTTCTCTTTTTCATTCTC
1 TTTT-TCTTTTTCATT-TC
*
29359114 TTTTTCTTTTTTGATTTC
1 TTTTTC-TTTTTCATTTC
29359132 TTTTTCT
1 TTTTTCT
29359139 GTCTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 10 0.43
19 12 0.52
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTCTTTTTCATTTC
Found at i:29360788 original size:30 final size:28
Alignment explanation
Indices: 29360754--29360809 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
29360744 GTGATTAAAT
29360754 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
29360784 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
29360810 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:29381703 original size:18 final size:17
Alignment explanation
Indices: 29381670--29381704 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
29381660 ATTTAAGTTA
*
29381670 TGATAAAAACATATTAT
1 TGATAAAAAAATATTAT
29381687 TGATAAAAAAATAATTAT
1 TGATAAAAAAAT-ATTAT
29381705 GTTGGATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (17 bp):
TGATAAAAAAATATTAT
Found at i:29388180 original size:67 final size:67
Alignment explanation
Indices: 29388072--29388202 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 67
29388062 GTAATTGTCA
*
29388072 TTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTATGCTC
29388137 TC
66 TC
* * *
29388139 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTTGCGGGAGTATGCT
1 TTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTATGCT
29388203 TTCTGAATTG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (67 bp):
TTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTATGCTC
TC
Found at i:29388698 original size:67 final size:67
Alignment explanation
Indices: 29388590--29388720 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 67
29388580 GTAATTGTCA
*
29388590 TTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTATGCTC
29388655 TC
66 TC
* * *
29388657 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTTGCGGGAGTATGCT
1 TTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTATGCT
29388721 TTCTGAATTG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (67 bp):
TTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTATGCTC
TC
Found at i:29388710 original size:518 final size:518
Alignment explanation
Indices: 29387733--29388767 Score: 2061
Period size: 518 Copynumber: 2.0 Consensus size: 518
29387723 AATTTAACCC
*
29387733 GGTAAGTTCGTGTAACTTGAATTATGTTCTTAAATGCTTGAAATGTATGTTATTGATGTGAATAT
1 GGTAAGTTCGTGTAACTTGAATTATATTCTTAAATGCTTGAAATGTATGTTATTGATGTGAATAT
29387798 GATTTGAATTTTCATTGTATGAAAATTGATAAAACATTGATATATTTGATAAAAAGGGAAAATAA
66 GATTTGAATTTTCATTGTATGAAAATTGATAAAACATTGATATATTTGATAAAAAGGGAAAATAA
29387863 ATCCCGGTTGAATGGAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGATCT
131 ATCCCGGTTGAATGGAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGATCT
29387928 AGCCCGGATGAGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATTTAGC
196 AGCCCGGATGAGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATTTAGC
29387993 CCAGACGGGTAATCCGAATTAGGGTCTGAATTTAGCCTGGACTGGTAATTTAGATCCAAGCTCAT
261 CCAGACGGGTAATCCGAATTAGGGTCTGAATTTAGCCTGGACTGGTAATTTAGATCCAAGCTCAT
29388058 CAGAGTAATTGTCATTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTC
326 CAGAGTAATTGTCATTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTC
29388123 GCGGGAGTGTGCTCTCTTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGT
391 GCGGGAGTGTGCTCTCTTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGT
29388188 TTGCGGGAGTATGCTTTCTGAATTGGAAAATGTGCGCACATGAATATGAATTGACAGACCCGG
456 TTGCGGGAGTATGCTTTCTGAATTGGAAAATGTGCGCACATGAATATGAATTGACAGACCCGG
29388251 GGTAAGTTCGTGTAACTTGAATTATATTCTTAAATGCTTGAAATGTATGTTATTGATGTGAATAT
1 GGTAAGTTCGTGTAACTTGAATTATATTCTTAAATGCTTGAAATGTATGTTATTGATGTGAATAT
29388316 GATTTGAATTTTCATTGTATGAAAATTGATAAAACATTGATATATTTGATAAAAAGGGAAAATAA
66 GATTTGAATTTTCATTGTATGAAAATTGATAAAACATTGATATATTTGATAAAAAGGGAAAATAA
29388381 ATCCCGGTTGAATGGAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGATCT
131 ATCCCGGTTGAATGGAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGATCT
29388446 AGCCCGGATGAGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATTTAGC
196 AGCCCGGATGAGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATTTAGC
29388511 CCAGACGGGTAATCCGAATTAGGGTCTGAATTTAGCCTGGACTGGTAATTTAGATCCAAGCTCAT
261 CCAGACGGGTAATCCGAATTAGGGTCTGAATTTAGCCTGGACTGGTAATTTAGATCCAAGCTCAT
29388576 CAGAGTAATTGTCATTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTC
326 CAGAGTAATTGTCATTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTC
29388641 GCGGGAGTGTGCTCTCTTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGT
391 GCGGGAGTGTGCTCTCTTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGT
29388706 TTGCGGGAGTATGCTTTCTGAATTGGAAAATGTGCGCACATGAATATGAATTGACAGACCCG
456 TTGCGGGAGTATGCTTTCTGAATTGGAAAATGTGCGCACATGAATATGAATTGACAGACCCG
29388768 AATTTGTACA
Statistics
Matches: 516, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
518 516 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (518 bp):
GGTAAGTTCGTGTAACTTGAATTATATTCTTAAATGCTTGAAATGTATGTTATTGATGTGAATAT
GATTTGAATTTTCATTGTATGAAAATTGATAAAACATTGATATATTTGATAAAAAGGGAAAATAA
ATCCCGGTTGAATGGAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGATCT
AGCCCGGATGAGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATTTAGC
CCAGACGGGTAATCCGAATTAGGGTCTGAATTTAGCCTGGACTGGTAATTTAGATCCAAGCTCAT
CAGAGTAATTGTCATTGCAGAGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTC
GCGGGAGTGTGCTCTCTTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGT
TTGCGGGAGTATGCTTTCTGAATTGGAAAATGTGCGCACATGAATATGAATTGACAGACCCGG
Found at i:29401956 original size:263 final size:261
Alignment explanation
Indices: 29401491--29402014 Score: 789
Period size: 263 Copynumber: 2.0 Consensus size: 261
29401481 CACCTTTTCT
* *
29401491 TATGAACAGAATTACTATCACGGTAATAGTCGTGCCCACGACTCGTGACAAGCTTGCTGAAAAAA
1 TATGAACAGAATTACTATCACAGTAATAGTCCTGCCCACGACTCGTGACAAGCTTGCTGAAAAAA
* ** *
29401556 AAGAAGTAAAATAAATGAGGGAATGAAAATGTTTGGGAAGTCAATAAAATGTAATAGCAGCAAAT
66 AAGAAATAAAATAAATGAGGGAATGAAAATGTTTGAAAAGTAAATAAAATGTAATAGCAGCAAAT
* * * *
29401621 AAAAATTATATTAATCGTAAATAAAAAAAGTAAATGGAGTTTAACTTCATAAGCAATAATATAAA
131 AAAAATTATATTAATCGAAAACAAAAAAAGTAAATAGAGTTGAACTTCATAAGCAATAATATAAA
*
29401686 GTCTTAGCCTTAAACTAGGTTAATTTTAGTTCTAAATCGATCATTGAAAATGAGTTTTCTCCTCC
196 GTCTTAGCCTTAAACTAGGTTAATTCTAGTTCTAAATCGATCATTGAAAATGAGTTTTCTCCTCC
29401751 A
261 A
* *
29401752 TATGAACAGAATTACTGTCGCAGTAATAGTCCTGCCCACGACTCGTG-CTAAGCTTGCTGAAAAA
1 TATGAACAGAATTACTATCACAGTAATAGTCCTGCCCACGACTCGTGAC-AAGCTTGCTGAAAAA
* *
29401816 AAAGAAATAAAATAAATAAGGGGGAATGAAAATGTTTGAAAAGTAAATAAAATGTAATAGTAGCA
65 AAAGAAATAAAATAAAT--GAGGGAATGAAAATGTTTGAAAAGTAAATAAAATGTAATAGCAGCA
* * * *
29401881 AATAACAATTATATTAATCGAAAACAAAATAAGTAAATAGAGTTGGACTTCGTAAGCAATAATAT
128 AATAAAAATTATATTAATCGAAAACAAAAAAAGTAAATAGAGTTGAACTTCATAAGCAATAATAT
* * * * * *
29401946 AAAGTCTTAGCCTTAGACTCGGTTAATTCTGGTTCTGAATCGATCCTTGAAAATGAGTTTTCTCT
193 AAAGTCTTAGCCTTAAACTAGGTTAATTCTAGTTCTAAATCGATCATTGAAAATGAGTTTTCTCC
29402011 TCCA
258 TCCA
29402015 CACCATAAGC
Statistics
Matches: 235, Mismatches: 25, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
260 1 0.00
261 74 0.31
263 160 0.68
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (261 bp):
TATGAACAGAATTACTATCACAGTAATAGTCCTGCCCACGACTCGTGACAAGCTTGCTGAAAAAA
AAGAAATAAAATAAATGAGGGAATGAAAATGTTTGAAAAGTAAATAAAATGTAATAGCAGCAAAT
AAAAATTATATTAATCGAAAACAAAAAAAGTAAATAGAGTTGAACTTCATAAGCAATAATATAAA
GTCTTAGCCTTAAACTAGGTTAATTCTAGTTCTAAATCGATCATTGAAAATGAGTTTTCTCCTCC
A
Found at i:29406229 original size:26 final size:25
Alignment explanation
Indices: 29406200--29406262 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
29406190 TCTTGTATAC
*
29406200 ATTAATATTATTAAGATAAGTATTAA
1 ATTAATATTATTAAGA-AACTATTAA
**
29406226 ATTAA-ATTTATTATTAAACTATTAA
1 ATTAATA-TTATTAAGAAACTATTAA
*
29406251 AATAATATTATT
1 ATTAATATTATT
29406263 TTTGGAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 18 0.58
26 13 0.42
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (25 bp):
ATTAATATTATTAAGAAACTATTAA
Found at i:29407368 original size:23 final size:23
Alignment explanation
Indices: 29407342--29407388 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
29407332 AGGATATCAT
*
29407342 TAACTCTTTAATTGAGCTATGAA
1 TAACTCTTTAATTGAACTATGAA
29407365 TAACTCTTTAATTGAACTATGAA
1 TAACTCTTTAATTGAACTATGAA
29407388 T
1 T
29407389 TCCACTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (23 bp):
TAACTCTTTAATTGAACTATGAA
Found at i:29416485 original size:22 final size:22
Alignment explanation
Indices: 29416458--29416501 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29416448 AAAGATAAAA
29416458 AAATATATATTATTCTTTTATC
1 AAATATATATTATTCTTTTATC
29416480 AAATATATATTATTCTTTTATC
1 AAATATATATTATTCTTTTATC
29416502 CAACTATGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATATATATTATTCTTTTATC
Found at i:29417118 original size:52 final size:52
Alignment explanation
Indices: 29417062--29417167 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
29417052 ACGACACTGG
* * * **
29417062 CCTTACTGTTGATCCGTGTTGCGACCACAATAAGTGCTTGTTGTGACATTGA
1 CCTTACTGTTGATCCATGTTACGACCACAACAAGTGCTTGTTGCAACATTGA
* * * *
29417114 CCTTATTGTTGGTCTATGTTATGACCACAACAAGTGCTTGTTGCAACATTGA
1 CCTTACTGTTGATCCATGTTACGACCACAACAAGTGCTTGTTGCAACATTGA
29417166 CC
1 CC
29417168 CCATTGAGTC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.35
Consensus pattern (52 bp):
CCTTACTGTTGATCCATGTTACGACCACAACAAGTGCTTGTTGCAACATTGA
Found at i:29421483 original size:16 final size:16
Alignment explanation
Indices: 29421458--29421558 Score: 157
Period size: 16 Copynumber: 6.3 Consensus size: 16
29421448 TTGGTTTGCT
*
29421458 GTAATAGAATAGAGGC
1 GTAATGGAATAGAGGC
**
29421474 GTAATGGAATAGAAAC
1 GTAATGGAATAGAGGC
*
29421490 GTAATGGTATAGAGGC
1 GTAATGGAATAGAGGC
*
29421506 GTAATGGAATAGAGAC
1 GTAATGGAATAGAGGC
29421522 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
29421538 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
29421554 GTAAT
1 GTAAT
29421559 AGCAATTCAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 76 1.00
ACGTcount: A:0.41, C:0.06, G:0.33, T:0.21
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:29421727 original size:21 final size:20
Alignment explanation
Indices: 29421703--29421789 Score: 53
Period size: 19 Copynumber: 4.5 Consensus size: 20
29421693 AATAAGATTA
29421703 TTAATATAAATAATAAATAAT
1 TTAATATAAATAA-AAATAAT
* *
29421724 TTAATAATAATTTAAAATAA-
1 TTAAT-ATAAATAAAAATAAT
* *
29421744 TT-AT-T-ATTAAATATAAT
1 TTAATATAAATAAAAATAAT
*
29421761 TTAATA-AAA-AATATATAAT
1 TTAATATAAATAA-AAATAAT
29421780 TTAATA-AAAT
1 TTAATATAAAT
29421790 TCTTAATATA
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
16 9 0.17
17 3 0.06
18 4 0.07
19 19 0.35
20 2 0.04
21 11 0.20
22 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATATAAATAAAAATAAT
Found at i:29421732 original size:11 final size:11
Alignment explanation
Indices: 29421713--29421745 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29421703 TTAATATAAA
29421713 TAATAAATAATT
1 TAAT-AATAATT
29421725 TAATAATAATT
1 TAATAATAATT
29421736 TAA-AATAATT
1 TAATAATAATT
29421746 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 10 0.48
12 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATT
Found at i:29421766 original size:24 final size:21
Alignment explanation
Indices: 29421690--29421802 Score: 79
Period size: 21 Copynumber: 5.1 Consensus size: 21
29421680 GTTATTAAAT
29421690 TTTAATAAGATTATTAATATAA
1 TTTAATAA-ATTATTAATATAA
* *
29421712 -ATAATAAATAATTTAATAATAA
1 TTTAATAAATTA-TTAAT-ATAA
29421734 TTTAAAATAATTATTATTAAATATAA
1 TTT--AATAA--ATTATT-AATATAA
* *
29421760 TTTAATAAA-AAAT-ATATAA
1 TTTAATAAATTATTAATATAA
*
29421779 TTTAATAAAATTCTTAATATAA
1 TTTAAT-AAATTATTAATATAA
29421801 TT
1 TT
29421803 ATTCTTATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 22
0.70 0.09 0.22
Matches are distributed among these distances:
19 12 0.17
20 6 0.08
21 14 0.20
22 13 0.18
23 1 0.01
24 5 0.07
25 5 0.07
26 9 0.13
27 6 0.08
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (21 bp):
TTTAATAAATTATTAATATAA
Found at i:29421769 original size:29 final size:28
Alignment explanation
Indices: 29421736--29421826 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 28
29421726 AATAATAATT
29421736 TAAAATAATTATTATTAAATATAATTTAA
1 TAAAATAATTATTATTAAATATAATTT-A
* * *
29421765 TAAAA-AATATATAATTTAATAAAATTCT-
1 TAAAATAAT-TATTATTAAATATAATT-TA
* * *
29421793 TAATATAATTATTCTTATAT-TAATTTA
1 TAAAATAATTATTATTAAATATAATTTA
29421820 CTAAAAT
1 -TAAAAT
29421827 CATAATATAT
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 19 0.40
29 22 0.47
30 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
TAAAATAATTATTATTAAATATAATTTA
Found at i:29421779 original size:56 final size:57
Alignment explanation
Indices: 29421703--29421831 Score: 156
Period size: 56 Copynumber: 2.3 Consensus size: 57
29421693 AATAAGATTA
29421703 TTAATATAAATAATAAATAATTTAATAATAA-T-TTAAAATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAA-AATTCTTAAAATAATTATTATTAAAT-TAAT
* * * *
29421761 TTAATAAAA-AATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATTAAT
1 TTAATAAAATAATAAATAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAAT
* *
29421817 TTACTAAAATCATAA
1 TTAATAAAATAATAA
29421832 TATATAATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
55 2 0.03
56 29 0.48
57 24 0.39
58 6 0.10
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (57 bp):
TTAATAAAATAATAAATAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAAT
Found at i:29422249 original size:77 final size:77
Alignment explanation
Indices: 29422122--29422283 Score: 306
Period size: 77 Copynumber: 2.1 Consensus size: 77
29422112 ATTTTTTGTC
*
29422122 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAACTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
29422187 TTATTGACATAA
66 TTATTGACATAA
*
29422199 CACTTTAATAACTGAACTTGACACTTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAACTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
29422264 TTATTGACATAA
66 TTATTGACATAA
29422276 CACTTTAA
1 CACTTTAA
29422284 GATTGTCTCA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 83 1.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (77 bp):
CACTTTAATAACTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
TTATTGACATAA
Found at i:29423581 original size:5 final size:5
Alignment explanation
Indices: 29423566--29423601 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
29423556 NNNNNNCCGG
* *
29423566 GGCCC GCCCC GACCC GGCCC GGCCC GGCCC GGCCC G
1 GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC G
29423602 ATATAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.03, C:0.61, G:0.36, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:29423654 original size:18 final size:17
Alignment explanation
Indices: 29423620--29423652 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29423610 AACATATTTA
29423620 TTTTTTAATTTTAAAAT
1 TTTTTTAATTTTAAAAT
29423637 TTTTTTAATTTTAAAA
1 TTTTTTAATTTTAAAA
29423653 ATAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTTAATTTTAAAAT
Found at i:29423661 original size:22 final size:24
Alignment explanation
Indices: 29423633--29423677 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
29423623 TTTAATTTTA
29423633 AAATTTTTT-TAATT-TTAAAAAT
1 AAATTTTTTGTAATTATTAAAAAT
*
29423655 AAATTTTTTGTATTTATTAAAAA
1 AAATTTTTTGTAATTATTAAAAA
29423678 AATAGGCCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
24 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
AAATTTTTTGTAATTATTAAAAAT
Found at i:29424294 original size:31 final size:31
Alignment explanation
Indices: 29424256--29424317 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
29424246 AGTTCCTTCA
29424256 AACAACACCCTTAGCAACAAAAATTAAGTTT
1 AACAACACCCTTAGCAACAAAAATTAAGTTT
29424287 AACAACACCCTTAGCAACAAAAATTAAGTTT
1 AACAACACCCTTAGCAACAAAAATTAAGTTT
29424318 TCTTTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (31 bp):
AACAACACCCTTAGCAACAAAAATTAAGTTT
Found at i:29424994 original size:15 final size:15
Alignment explanation
Indices: 29424974--29425002 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29424964 ATGAAGGAAA
29424974 AAAGGGAAATAAGAT
1 AAAGGGAAATAAGAT
29424989 AAAGGGAAATAAGA
1 AAAGGGAAATAAGA
29425003 AGGAAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (15 bp):
AAAGGGAAATAAGAT
Found at i:29429544 original size:22 final size:20
Alignment explanation
Indices: 29429498--29429568 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 20
29429488 ATATTATAAT
29429498 AAAAGAAAAGAAATAGAAAAAGA
1 AAAAG-AAAG-AA-AGAAAAAGA
29429521 AAAAGAAAGAAAGAACAAACGA
1 AAAAGAAAGAAAGAA-AAA-GA
*
29429543 AACAGAAAGGAAA-AAGAAAGA
1 AAAAGAAA-GAAAGAA-AAAGA
29429564 AAAAG
1 AAAAG
29429569 GAATAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.10
21 11 0.26
22 18 0.43
23 9 0.21
ACGTcount: A:0.75, C:0.04, G:0.20, T:0.01
Consensus pattern (20 bp):
AAAAGAAAGAAAGAAAAAGA
Found at i:29429560 original size:11 final size:10
Alignment explanation
Indices: 29429516--29429568 Score: 61
Period size: 11 Copynumber: 5.0 Consensus size: 10
29429506 AGAAATAGAA
29429516 AAAGAAAAAG
1 AAAGAAAAAG
*
29429526 AAAGAAAGAAC
1 AAAGAAA-AAG
*
29429537 AAACGAAACAG
1 AAA-GAAAAAG
29429548 AAAGGAAAAAG
1 AAA-GAAAAAG
29429559 AAAGAAAAAG
1 AAAGAAAAAG
29429569 GAATAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 14 0.39
11 18 0.50
12 4 0.11
ACGTcount: A:0.74, C:0.06, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:29429585 original size:28 final size:29
Alignment explanation
Indices: 29429526--29429587 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
29429516 AAAGAAAAAG
*
29429526 AAAGAAAGAACAAACGAAACAGAAAGGAA
1 AAAGAAAGAACAAACGAAACAAAAAGGAA
*
29429555 AAAGAAAGAA-AAAGGAATA-AAAAAGGAA
1 AAAGAAAGAACAAACGAA-ACAAAAAGGAA
29429583 AAAGA
1 AAAGA
29429588 CCAAATTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.73, C:0.05, G:0.21, T:0.02
Consensus pattern (29 bp):
AAAGAAAGAACAAACGAAACAAAAAGGAA
Found at i:29429940 original size:40 final size:40
Alignment explanation
Indices: 29429894--29429972 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
29429884 AGGTGCCAAT
**
29429894 TTACTTTGGTTTAGCCGATGAGACACTGGGTGTCAAACTA
1 TTACTTTGAATTAGCCGATGAGACACTGGGTGTCAAACTA
* * *
29429934 TTACTTTGAATTATCCGATGAGGCATTGGGTGTCAAACT
1 TTACTTTGAATTAGCCGATGAGACACTGGGTGTCAAACT
29429973 GGTGTGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (40 bp):
TTACTTTGAATTAGCCGATGAGACACTGGGTGTCAAACTA
Found at i:29442598 original size:40 final size:40
Alignment explanation
Indices: 29442494--29442786 Score: 202
Period size: 40 Copynumber: 7.3 Consensus size: 40
29442484 ACTAGCATTT
* *
29442494 AGCCTACTAAGCACTAA--TTGATAAATTCACCAGCACAA
1 AGCCTGCTAAGCACTAAGCTTGATAAATACACCAGCACAA
* ** * * *
29442532 AGCCCTGCTAGGCAC-AACGCCCGATAACTACACCGGCAGAA
1 AG-CCTGCTAAGCACTAA-GCTTGATAAATACACCAGCACAA
* * * *
29442573 AGCCTGCTAAACACTAAGCTTGATAAATTCATCAACACAA
1 AGCCTGCTAAGCACTAAGCTTGATAAATACACCAGCACAA
* * * * *
29442613 AGCCTGCTAGGCACAAAACCTT-ATAACTACACCATCACAA
1 AGCCTGCTAAGCAC-TAAGCTTGATAAATACACCAGCACAA
* * * * *
29442653 AGCTTGCTAAACATTAAGCTTGATAAATTCACCAGCACGA
1 AGCCTGCTAAGCACTAAGCTTGATAAATACACCAGCACAA
* ** *
29442693 AGCCTGGTGGGCAC-AGAGCTTGATAACTACACC-GACACAA
1 AGCCTGCTAAGCACTA-AGCTTGATAAATACACCAG-CACAA
* * * * *
29442733 AGCTTGTTAAGCACTAAGCTTGATAAATTCATCGGCACAA
1 AGCCTGCTAAGCACTAAGCTTGATAAATACACCAGCACAA
* *
29442773 AACCTGCTAGGCAC
1 AGCCTGCTAAGCAC
29442787 AAAGTCCGAT
Statistics
Matches: 188, Mismatches: 56, Indels: 20
0.71 0.21 0.08
Matches are distributed among these distances:
38 4 0.02
39 17 0.09
40 141 0.75
41 26 0.14
ACGTcount: A:0.37, C:0.28, G:0.16, T:0.19
Consensus pattern (40 bp):
AGCCTGCTAAGCACTAAGCTTGATAAATACACCAGCACAA
Found at i:29442798 original size:80 final size:79
Alignment explanation
Indices: 29442511--29442798 Score: 344
Period size: 80 Copynumber: 3.6 Consensus size: 79
29442501 TAAGCACTAA
* * *
29442511 TTGATAAATTCACCAGCACAAAGCCCTGCTAGGCACAACGCCCGATAACTACACCGGCAGAAAGC
1 TTGATAAATTCACCAGCACAAAG-CCTGCTAGGCACAAAG-CCGATAACTACACCGACACAAAGC
*
29442576 CTGCTAAACACTAAGC
64 TTGCTAAACACTAAGC
* * * *
29442592 TTGATAAATTCATCAACACAAAGCCTGCTAGGCACAAAACCTTATAACTACACC-ATCACAAAGC
1 TTGATAAATTCACCAGCACAAAGCCTGCTAGGCACAAAGCC-GATAACTACACCGA-CACAAAGC
*
29442656 TTGCTAAACATTAAGC
64 TTGCTAAACACTAAGC
* * * * *
29442672 TTGATAAATTCACCAGCACGAAGCCTGGTGGGCACAGAGCTTGATAACTACACCGACACAAAGCT
1 TTGATAAATTCACCAGCACAAAGCCTGCTAGGCACAAAGC-CGATAACTACACCGACACAAAGCT
* *
29442737 TGTTAAGCACTAAGC
65 TGCTAAACACTAAGC
* * *
29442752 TTGATAAATTCATCGGCACAAAACCTGCTAGGCACAAAGTCCGATAA
1 TTGATAAATTCACCAGCACAAAGCCTGCTAGGCACAAAG-CCGATAA
29442799 TTTCATAACA
Statistics
Matches: 173, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
79 2 0.01
80 148 0.86
81 23 0.13
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.19
Consensus pattern (79 bp):
TTGATAAATTCACCAGCACAAAGCCTGCTAGGCACAAAGCCGATAACTACACCGACACAAAGCTT
GCTAAACACTAAGC
Found at i:29444009 original size:15 final size:14
Alignment explanation
Indices: 29443985--29444027 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
29443975 GTCACATCCC
29443985 AAAATCTGGGTTAGTA
1 AAAAT-TGGGTTA-TA
29444001 AAAATTGGGTTCATA
1 AAAATTGGGTT-ATA
*
29444016 AAAATTAGGTTA
1 AAAATTGGGTTA
29444028 ATGAACCGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 1 0.04
15 18 0.72
16 6 0.24
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.33
Consensus pattern (14 bp):
AAAATTGGGTTATA
Found at i:29445942 original size:24 final size:24
Alignment explanation
Indices: 29445862--29445936 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
29445852 GAGGAAAAAT
*
29445862 TGGTGGCTTCATCCACAACCTACG
1 TGGTGGCTTCATCCACAACCTACA
* *
29445886 TGGTGGCTTCCTCCACGACCTACA
1 TGGTGGCTTCATCCACAACCTACA
*
29445910 TGGTGGCTTCGTCCACAACCTACA
1 TGGTGGCTTCATCCACAACCTACA
29445934 TGG
1 TGG
29445937 CAGCTTATCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.19, C:0.33, G:0.23, T:0.25
Consensus pattern (24 bp):
TGGTGGCTTCATCCACAACCTACA
Found at i:29447630 original size:24 final size:24
Alignment explanation
Indices: 29447603--29447683 Score: 108
Period size: 24 Copynumber: 3.4 Consensus size: 24
29447593 GAAGAAGAAT
* *
29447603 TGGTGGCTTTGTCCACAACCTACG
1 TGGTGGCTTCGTCCACAACCTACA
* *
29447627 TGGTGGCTTCCTCCACGACCTACA
1 TGGTGGCTTCGTCCACAACCTACA
*
29447651 TGGTGGCTTCGTTCACAACCTACA
1 TGGTGGCTTCGTCCACAACCTACA
*
29447675 TGGTAGCTT
1 TGGTGGCTT
29447684 ATTTGCAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.30
Consensus pattern (24 bp):
TGGTGGCTTCGTCCACAACCTACA
Found at i:29449063 original size:11 final size:11
Alignment explanation
Indices: 29449049--29449074 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29449039 ATTTTTTTAA
29449049 TTTTAAAATAC
1 TTTTAAAATAC
29449060 TTTTAAAATAC
1 TTTTAAAATAC
29449071 TTTT
1 TTTT
29449075 TTTAAAATTT
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:29449118 original size:13 final size:11
Alignment explanation
Indices: 29449049--29449156 Score: 51
Period size: 11 Copynumber: 10.4 Consensus size: 11
29449039 ATTTTTTTAA
*
29449049 TTTTAAAATAC
1 TTTTAAAATAT
29449060 TTTTAAAATACTTT
1 TTTTAAAATA---T
29449074 TTTTAAAAT-T
1 TTTTAAAATAT
*
29449084 TTTT----TAA
1 TTTTAAAATAT
29449091 TTTTAAAATAT
1 TTTTAAAATAT
29449102 TTTTAAAATACAT
1 TTTTAAAAT--AT
29449115 TTTT--AAT-T
1 TTTTAAAATAT
*
29449123 TTTT----TAA
1 TTTTAAAATAT
29449130 TTTTAAAATAT
1 TTTTAAAATAT
29449141 TTTTAAAATAAT
1 TTTTAAAAT-AT
29449153 TTTT
1 TTTT
29449157 TTTAATTTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 31
0.68 0.04 0.28
Matches are distributed among these distances:
6 2 0.03
7 8 0.11
8 5 0.07
10 5 0.07
11 35 0.46
12 6 0.08
13 6 0.08
14 9 0.12
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:29449167 original size:39 final size:39
Alignment explanation
Indices: 29449032--29449168 Score: 161
Period size: 39 Copynumber: 3.4 Consensus size: 39
29449022 AATATTTTTA
* * *
29449032 TTTTTTTATTTTTTTAATTTTAAAATACTTTTAAAATACT
1 TTTTTTTA-ATTTTTAATTTTAAAATATTTTTAAAATAAT
*
29449072 TTTTTTAAAATTTTTTTAATTTTAAAATATTTTTAAAATACAT
1 TTTTTT-TAA--TTTTTAATTTTAAAATATTTTTAAAATA-AT
*
29449115 TTTTAATT--TTTTTAATTTTAAAATATTTTTAAAATAAT
1 TTTT-TTTAATTTTTAATTTTAAAATATTTTTAAAATAAT
29449153 TTTTTTTAATTTTTAA
1 TTTTTTTAATTTTTAA
29449169 AATAAATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
37 2 0.02
38 6 0.07
39 35 0.42
40 6 0.07
41 1 0.01
42 27 0.33
43 5 0.06
44 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTTTTTAATTTTTAATTTTAAAATATTTTTAAAATAAT
Found at i:29449186 original size:22 final size:21
Alignment explanation
Indices: 29449138--29449186 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
29449128 AATTTTAAAA
**
29449138 TATTTTTAAAATAATTTTTTT
1 TATTTTTAAAATAATTTTTGG
29449159 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTTGG
29449182 TATTT
1 TATTT
29449187 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
TATTTTTAAAATAATTTTTGG
Found at i:29454615 original size:3 final size:3
Alignment explanation
Indices: 29454607--29454639 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
29454597 AGGCAAGCAA
29454607 GAT GAT GAT GAT GAT GAT GAT GA- GAT AGAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT -GAT GAT
29454640 TTTGGGTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:29455496 original size:54 final size:56
Alignment explanation
Indices: 29455432--29455540 Score: 195
Period size: 54 Copynumber: 2.0 Consensus size: 56
29455422 AATGTTGTTT
29455432 CTGGTTAAGTGTAATTGACTCCATTTTCTTTCTA-CAAAAA-AAAAAGATTCAAAA
1 CTGGTTAAGTGTAATTGACTCCATTTTCTTTCTACCAAAAAGAAAAAGATTCAAAA
*
29455486 CTGGTTAAGTGTAATTGACTCTATTTTCTTTCTACCAAAAAGAAAAAGATTCAAA
1 CTGGTTAAGTGTAATTGACTCCATTTTCTTTCTACCAAAAAGAAAAAGATTCAAA
29455541 TCTTGTTATT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
54 33 0.63
55 6 0.12
56 13 0.25
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (56 bp):
CTGGTTAAGTGTAATTGACTCCATTTTCTTTCTACCAAAAAGAAAAAGATTCAAAA
Found at i:29455569 original size:56 final size:54
Alignment explanation
Indices: 29455432--29455567 Score: 139
Period size: 54 Copynumber: 2.5 Consensus size: 54
29455422 AATGTTGTTT
* * **
29455432 CTGGTTAAGTGTAATTGACTCCATTTTCTTTCTACAAAAAAAAAAGATTCAAAA
1 CTGGTTAAGTATAATCGACTATATTTTCTTTCTACAAAAAAAAAAGATTCAAAA
* * * *
29455486 CTGGTTAAGTGTAATTGACTCTATTTTCTTTCTACCAAAAAGAAAAAGATTCAAAT
1 CTGGTTAAGTATAATCGACTATATTTTCTTTCTA-CAAAAA-AAAAAGATTCAAAA
* * * *
29455542 CTTGTT-ATTATCATCGAGTATATTTT
1 CTGGTTAAGTATAATCGACTATATTTT
29455568 TCATTCATGA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
54 33 0.46
55 20 0.28
56 18 0.25
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (54 bp):
CTGGTTAAGTATAATCGACTATATTTTCTTTCTACAAAAAAAAAAGATTCAAAA
Found at i:29458293 original size:22 final size:22
Alignment explanation
Indices: 29458244--29458298 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
29458234 ATTTAATTAA
*
29458244 ATTATTTA-AAATAATTAATTT
1 ATTATTTATAAATAAATAATTT
* *
29458265 ATAATTTATAAATAAATATTTT
1 ATTATTTATAAATAAATAATTT
*
29458287 TTTATTTTATAA
1 ATTA-TTTATAA
29458299 TTTTTAATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 7 0.26
22 13 0.48
23 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTATTTATAAATAAATAATTT
Found at i:29463486 original size:81 final size:81
Alignment explanation
Indices: 29463351--29463515 Score: 285
Period size: 81 Copynumber: 2.0 Consensus size: 81
29463341 AAATAAGTAA
* * * *
29463351 TTTTAATCAATTAACCACTTTTAGTGTTCAATTTAATCCACATTTCATATTTATGTAAAATTACC
1 TTTTAATCAATTAACCACTTCTAGTATTCAATTTAATCAACATTTCATATTTATGCAAAATTACC
*
29463416 AATTTACCCCTAATAT
66 AATTTACCCCAAATAT
29463432 TTTTAATCAATTAACCACTTCTAGTATTCAATTTAATCAACATTTCATATTTATGCAAAATTACC
1 TTTTAATCAATTAACCACTTCTAGTATTCAATTTAATCAACATTTCATATTTATGCAAAATTACC
29463497 AATTTACCCCAAATAT
66 AATTTACCCCAAATAT
29463513 TTT
1 TTT
29463516 AACTTTTTCA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (81 bp):
TTTTAATCAATTAACCACTTCTAGTATTCAATTTAATCAACATTTCATATTTATGCAAAATTACC
AATTTACCCCAAATAT
Found at i:29465174 original size:59 final size:61
Alignment explanation
Indices: 29465103--29465219 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 61
29465093 ATCACTTTAA
* * *
29465103 TATTAAATTAATATAATATTTA-T-CAACATAAATATTAGA-TTAAGTTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTACTACAACATAAATATTAAATTTAA-TTTAATATTAAATCT
* *
29465162 TATTAAAATAATAGAATGTTTATCTACAAGATAAATATTAAATTTAATTTAATATTAA
1 TATTAAAATAATAGAATATTTA-CTACAACATAAATATTAAATTTAATTTAATATTAA
29465220 GATAATCAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 19 0.39
61 1 0.02
62 25 0.51
63 4 0.08
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (61 bp):
TATTAAAATAATAGAATATTTACTACAACATAAATATTAAATTTAATTTAATATTAAATCT
Found at i:29472240 original size:16 final size:16
Alignment explanation
Indices: 29472219--29472250 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29472209 AGAAACGAGT
29472219 TTGGAAAACGCAGCGA
1 TTGGAAAACGCAGCGA
29472235 TTGGAAAACGCAGCGA
1 TTGGAAAACGCAGCGA
29472251 AAAATAAATT
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:0.38, C:0.19, G:0.31, T:0.12
Consensus pattern (16 bp):
TTGGAAAACGCAGCGA
Found at i:29480316 original size:44 final size:44
Alignment explanation
Indices: 29480253--29480339 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
29480243 AAGACAATTG
*
29480253 GTTAATGCGTCTAACCTTCCTCTATCAAGTGACTAGATTTTTTA
1 GTTAATGCGTCTAACCTTCCCCTATCAAGTGACTAGATTTTTTA
* *
29480297 GTTAATGCGTTTAACCTTCCCCTATCAAGTGACTGGATTTTTT
1 GTTAATGCGTCTAACCTTCCCCTATCAAGTGACTAGATTTTTT
29480340 TACACACTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (44 bp):
GTTAATGCGTCTAACCTTCCCCTATCAAGTGACTAGATTTTTTA
Found at i:29482249 original size:51 final size:52
Alignment explanation
Indices: 29482181--29482291 Score: 136
Period size: 51 Copynumber: 2.2 Consensus size: 52
29482171 TTATAAAACT
* * * *
29482181 TATATATATATATATATAAAATACA-TAATGCATTTATGAAAACAAGGAAA-A
1 TATAAATATATACATATAAAATACATTAATGCATTTA-CAAAAAAAGGAAATA
* * *
29482232 TATAAATATATACATATAAAATATATTCATGCATTTACAAAAAAATGAAATA
1 TATAAATATATACATATAAAATACATTAATGCATTTACAAAAAAAGGAAATA
29482284 TATAAATA
1 TATAAATA
29482292 AGGAAATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 32 0.63
52 19 0.37
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.32
Consensus pattern (52 bp):
TATAAATATATACATATAAAATACATTAATGCATTTACAAAAAAAGGAAATA
Found at i:29482341 original size:228 final size:228
Alignment explanation
Indices: 29482058--29482519 Score: 915
Period size: 228 Copynumber: 2.0 Consensus size: 228
29482048 ATCAATAAGC
29482058 AAATGAAGGAAATAAACAAAAAAAATATAAAGAGAAAAAGGTACAAAATATATATACATTCGAAA
1 AAAT-AAGGAAATAAACAAAAAAAATATAAAGAGAAAAAGGTACAAAATATATATACATTCGAAA
29482123 TTATGAAGAATAAAAGACATAAAGATAATTTACTTATAAAATTTTGGGTTATAAAACTTATATAT
65 TTATGAAGAATAAAAGACATAAAGATAATTTACTTATAAAATTTTGGGTTATAAAACTTATATAT
29482188 ATATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATATACATATAAAA
130 ATATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATATACATATAAAA
29482253 TATATTCATGCATTTACAAAAAAATGAAATATAT
195 TATATTCATGCATTTACAAAAAAATGAAATATAT
29482287 AAATAAGGAAATAAACAAAAAAAATATAAAGAGAAAAAGGTACAAAATATATATACATTCGAAAT
1 AAATAAGGAAATAAACAAAAAAAATATAAAGAGAAAAAGGTACAAAATATATATACATTCGAAAT
29482352 TATGAAGAATAAAAGACATAAAGATAATTTACTTATAAAATTTTGGGTTATAAAACTTATATATA
66 TATGAAGAATAAAAGACATAAAGATAATTTACTTATAAAATTTTGGGTTATAAAACTTATATATA
29482417 TATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATATACATATAAAAT
131 TATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATATACATATAAAAT
29482482 ATATTCATGCATTTACAAAAAAATGAAATATAT
196 ATATTCATGCATTTACAAAAAAATGAAATATAT
29482515 AAATA
1 AAATA
29482520 TAATATAAAA
Statistics
Matches: 233, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
228 229 0.98
229 4 0.02
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (228 bp):
AAATAAGGAAATAAACAAAAAAAATATAAAGAGAAAAAGGTACAAAATATATATACATTCGAAAT
TATGAAGAATAAAAGACATAAAGATAATTTACTTATAAAATTTTGGGTTATAAAACTTATATATA
TATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATATACATATAAAAT
ATATTCATGCATTTACAAAAAAATGAAATATAT
Found at i:29482477 original size:51 final size:52
Alignment explanation
Indices: 29482409--29482521 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 52
29482399 TTATAAAACT
* * * *
29482409 TATATATATATATATATAAAATACA-TAATGCATTTATGAAAACAAGGAAA-A
1 TATAAATATATACATATAAAATACATTAATGCATTTA-CAAAAAAAGGAAATA
* * *
29482460 TATAAATATATACATATAAAATATATTCATGCATTTACAAAAAAATGAAATA
1 TATAAATATATACATATAAAATACATTAATGCATTTACAAAAAAAGGAAATA
29482512 TATAAATATA
1 TATAAATATA
29482522 ATATAAAACG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 32 0.60
52 21 0.40
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.33
Consensus pattern (52 bp):
TATAAATATATACATATAAAATACATTAATGCATTTACAAAAAAAGGAAATA
Found at i:29482794 original size:3 final size:3
Alignment explanation
Indices: 29482786--29482828 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
29482776 ATATGTAGGT
29482786 ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29482829 CAAAATTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:29482801 original size:24 final size:21
Alignment explanation
Indices: 29482785--29482827 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
29482775 TATATGTAGG
29482785 TATAATAATAATAATATATAA
1 TATAATAATAATAATATATAA
29482806 TATAATAATAATAATA-ATAA
1 TATAATAATAATAATATATAA
29482826 TA
1 TA
29482828 ACAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TATAATAATAATAATATATAA
Found at i:29482838 original size:27 final size:27
Alignment explanation
Indices: 29482786--29482844 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
29482776 ATATGTAGGT
* *
29482786 ATAATAATAATAATATATAATATAATA
1 ATAATAATAATAATACAAAATATAATA
29482813 ATAATAATAATAATAACAAAAT-TAATA
1 ATAATAATAATAAT-ACAAAATATAATA
29482840 A-AATA
1 ATAATA
29482845 GACTAAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 20 0.69
28 5 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
ATAATAATAATAATACAAAATATAATA
Found at i:29483229 original size:21 final size:21
Alignment explanation
Indices: 29483192--29483274 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
29483182 ATTATAAAAT
*
29483192 TATATC-T-TCTAAGATTGTA
1 TATATCATATCTAAAATTGTA
*
29483211 TATATCATATCTAAAATTGCA
1 TATATCATATCTAAAATTGTA
* *
29483232 TATATCATACCTAAGATTG--
1 TATATCATATCTAAAATTGTA
*
29483251 CATATCATATCTAAAATTGTA
1 TATATCATATCTAAAATTGTA
29483272 TAT
1 TAT
29483275 CTTCGAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
19 22 0.42
20 1 0.02
21 29 0.56
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (21 bp):
TATATCATATCTAAAATTGTA
Found at i:29483275 original size:19 final size:19
Alignment explanation
Indices: 29483211--29483275 Score: 85
Period size: 19 Copynumber: 3.3 Consensus size: 19
29483201 TAAGATTGTA
29483211 TATATCATATCTAAAATTG
1 TATATCATATCTAAAATTG
* *
29483230 CATATATCATACCTAAGATTG
1 --TATATCATATCTAAAATTG
*
29483251 CATATCATATCTAAAATTG
1 TATATCATATCTAAAATTG
29483270 TATATC
1 TATATC
29483276 TTCGAAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 21 0.55
21 17 0.45
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (19 bp):
TATATCATATCTAAAATTG
Found at i:29488227 original size:9 final size:9
Alignment explanation
Indices: 29488215--29488245 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29488205 ATTGAAAATT
29488215 TTGAGAGAA
1 TTGAGAGAA
29488224 TTGAGAGAA
1 TTGAGAGAA
*
29488233 TGGAGAGAA
1 TTGAGAGAA
29488242 TTGA
1 TTGA
29488246 ATTTGAGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:29488958 original size:21 final size:21
Alignment explanation
Indices: 29488919--29488992 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
29488909 AAATTGAAAA
*
29488919 TCAATTTGA-TTTGATTTTAT
1 TCAAATTGATTTTGATTTTAT
* * *
29488939 TCAACTTTATTTTTATTTTAT
1 TCAAATTGATTTTGATTTTAT
29488960 TCAAATTGATTTTGATTTTAT
1 TCAAATTGATTTTGATTTTAT
*
29488981 TCAAACTGATTT
1 TCAAATTGATTT
29488993 AAAGGTTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 7 0.15
21 39 0.85
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (21 bp):
TCAAATTGATTTTGATTTTAT
Found at i:29489746 original size:27 final size:26
Alignment explanation
Indices: 29489698--29489748 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
29489688 TAAATTTTGA
* *
29489698 TTTTTTTATAAATAAATTTAATAAAG
1 TTTTTTTAAAAATAAATATAATAAAG
29489724 TTTTTTTAAAAATAAATAATAATAA
1 TTTTTTTAAAAATAAAT-ATAATAA
29489749 TCAATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTTTTTAAAAATAAATATAATAAAG
Found at i:29491396 original size:17 final size:17
Alignment explanation
Indices: 29491374--29491407 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29491364 CTCCAAAGTC
*
29491374 TCTATTTATAGGTATAA
1 TCTATTTATAGGCATAA
29491391 TCTATTTATAGGCATAA
1 TCTATTTATAGGCATAA
29491408 GAAGTATAAA
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:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (17 bp):
TCTATTTATAGGCATAA
Found at i:29509235 original size:36 final size:34
Alignment explanation
Indices: 29509189--29509278 Score: 126
Period size: 36 Copynumber: 2.5 Consensus size: 34
29509179 TTATATATGC
* *
29509189 ATATGTGTATAAAAAATAGTTTAATATAAATTGTAT
1 ATATATGTATAAAAAATAGTTTAATACAAA-T-TAT
29509225 ATATATGTATAATAAAAATAGTTTAATACAAATTAT
1 ATATATGTAT-A-AAAAATAGTTTAATACAAATTAT
29509261 ATATATGTATAAAAAATA
1 ATATATGTATAAAAAATA
29509279 TTATGTAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
34 7 0.14
35 1 0.02
36 22 0.44
37 2 0.04
38 18 0.36
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (34 bp):
ATATATGTATAAAAAATAGTTTAATACAAATTAT
Found at i:29511496 original size:87 final size:87
Alignment explanation
Indices: 29511321--29511496 Score: 210
Period size: 87 Copynumber: 2.0 Consensus size: 87
29511311 AGCTATTCCA
** * * **
29511321 AGTCTTAATGCTAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTACTCTGCTGCAATGCCAA
1 AGTCTTAACACTAGGGAGATAAGATTCCCTGCCCTCAGCTTTAATCTACTCCGCTGCAACACCAA
** * *
29511386 GTAAGTAAGACTAATTACTTTT
66 GTAAACAAGACTAACTACCTTT
*
29511408 AGTCTTAACACTAGGGAGATAAGATTCCCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACC-A
1 AGTCTTAACACTAGGGAGATAAGATTCCCTGCCCTCAGCTTTAATCTACTCCGCTGCAACACCAA
* **
29511472 GTGAAACAAGATTCGCTACCTTT
66 GT-AAACAAGACTAACTACCTTT
29511495 AG
1 AG
29511497 CTTTAATCTG
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
86 3 0.04
87 71 0.96
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (87 bp):
AGTCTTAACACTAGGGAGATAAGATTCCCTGCCCTCAGCTTTAATCTACTCCGCTGCAACACCAA
GTAAACAAGACTAACTACCTTT
Found at i:29513051 original size:65 final size:65
Alignment explanation
Indices: 29512928--29513059 Score: 180
Period size: 65 Copynumber: 2.0 Consensus size: 65
29512918 CTCTCTATTT
* *
29512928 TCTTTTCTTTTCTTATTTTTTATTTTTTTTGGACTCAAAGAGCCCTTTGAGGGTTTTCACCTTGG
1 TCTTTTCTTTTCTTATTTTTTATTTTTTTTGGAATCAAAGAGCCCTTTGACGGTTTTCACCTTGG
* *
29512993 TCTTTT-TTTTGTT-TTTTTCTATCTTTTTTTAGGAATCAAAGCGCCCTTTG-CGGTTTTCACCT
1 TCTTTTCTTTTCTTATTTTT-TAT-TTTTTTT-GGAATCAAAGAGCCCTTTGACGGTTTTCACCT
29513055 TGG
63 TGG
29513058 TC
1 TC
29513060 CCTTCTCATT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
63 5 0.08
64 9 0.15
65 29 0.48
66 17 0.28
ACGTcount: A:0.13, C:0.18, G:0.15, T:0.54
Consensus pattern (65 bp):
TCTTTTCTTTTCTTATTTTTTATTTTTTTTGGAATCAAAGAGCCCTTTGACGGTTTTCACCTTGG
Found at i:29513961 original size:30 final size:29
Alignment explanation
Indices: 29513908--29514014 Score: 87
Period size: 30 Copynumber: 3.7 Consensus size: 29
29513898 TGGCCTCTCC
*
29513908 TTTTCCTTTTC-TTTTTCTT-TTTTC-TTT
1 TTTTCATTTTCATTTTT-TTATTTTCATTT
29513935 TTTCATCATTTTCATTTTTTTATTTTCATTT
1 TTT--TCATTTTCATTTTTTTATTTTCATTT
* * *
29513966 TTTTGATTTTGATTTTTTTTATTTT-TTTAT
1 TTTTCATTTTCA-TTTTTTTATTTTCATT-T
* *
29513996 TTTTGATTTTGATTTTTTT
1 TTTTCATTTTCATTTTTTT
29514015 TGATTGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
27 3 0.04
29 25 0.36
30 35 0.51
31 6 0.09
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.78
Consensus pattern (29 bp):
TTTTCATTTTCATTTTTTTATTTTCATTT
Found at i:29513967 original size:15 final size:15
Alignment explanation
Indices: 29513942--29514015 Score: 82
Period size: 15 Copynumber: 5.0 Consensus size: 15
29513932 TTTTTTCATC
29513942 ATTTTCA-TTTTTTT
1 ATTTTCATTTTTTTT
*
29513956 ATTTTCATTTTTTTG
1 ATTTTCATTTTTTTT
*
29513971 ATTTTGATTTTTTTT
1 ATTTTCATTTTTTTT
29513986 ATTTT--TTTATTTTT
1 ATTTTCATTT-TTTTT
*
29514000 GATTTTGATTTTTTTT
1 -ATTTTCATTTTTTTT
29514016 GATTGAATCT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
13 3 0.06
14 12 0.23
15 29 0.56
16 5 0.10
17 3 0.06
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (15 bp):
ATTTTCATTTTTTTT
Found at i:29513969 original size:23 final size:23
Alignment explanation
Indices: 29513919--29514014 Score: 74
Period size: 23 Copynumber: 4.2 Consensus size: 23
29513909 TTTCCTTTTC
* *
29513919 TTTTTC-TTTTTTCTTTTTTCATC
1 TTTTTCATTTTTT-TATTTTCATT
*
29513942 ATTTTCATTTTTTTATTTTCATT
1 TTTTTCATTTTTTTATTTTCATT
* *
29513965 TTTTTGATTTTGATTT-TTTTTATT
1 TTTTTCATTTT--TTTATTTTCATT
* *
29513989 TTTTT-A-TTTTTGATTTTGATT
1 TTTTTCATTTTTTTATTTTCATT
29514010 TTTTT
1 TTTTT
29514015 TGATTGAATC
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.03
21 12 0.20
22 3 0.05
23 23 0.38
24 18 0.30
25 3 0.05
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTTTCATTTTTTTATTTTCATT
Found at i:29513989 original size:24 final size:26
Alignment explanation
Indices: 29513952--29514011 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
29513942 ATTTTCATTT
29513952 TTTTATTTTCATTTTTTTGA-TTTTGA
1 TTTTATTTTCATTTTTTT-ATTTTTGA
29513978 TTTT-TTTT-ATTTTTTTATTTTTGA
1 TTTTATTTTCATTTTTTTATTTTTGA
29514002 TTTTGATTTT
1 TTTT-ATTTT
29514012 TTTTGATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.03
24 18 0.58
25 4 0.13
26 8 0.26
ACGTcount: A:0.13, C:0.02, G:0.07, T:0.78
Consensus pattern (26 bp):
TTTTATTTTCATTTTTTTATTTTTGA
Found at i:29514015 original size:30 final size:30
Alignment explanation
Indices: 29513949--29514015 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 30
29513939 ATCATTTTCA
29513949 TTTTTTTATTTTCATTTTTTTGATTTTGAT
1 TTTTTTTATTTTCATTTTTTTGATTTTGAT
*
29513979 TTTTTTTATTTT-TTTATTTTTGATTTTGAT
1 TTTTTTTATTTTCATT-TTTTTGATTTTGAT
29514009 TTTTTTT
1 TTTTTTT
29514016 GATTGAATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 2 0.06
30 33 0.94
ACGTcount: A:0.12, C:0.01, G:0.06, T:0.81
Consensus pattern (30 bp):
TTTTTTTATTTTCATTTTTTTGATTTTGAT
Found at i:29518430 original size:33 final size:33
Alignment explanation
Indices: 29518392--29518460 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
29518382 ATAATAATAT
29518392 ATAACAATATATGTAAAAGCTAAAATAAATAAA
1 ATAACAATATATGTAAAAGCTAAAATAAATAAA
*
29518425 ATAACAATATATGTAAAAGCTGAAATAAATAAA
1 ATAACAATATATGTAAAAGCTAAAATAAATAAA
29518458 ATA
1 ATA
29518461 TATTTAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.62, C:0.06, G:0.07, T:0.25
Consensus pattern (33 bp):
ATAACAATATATGTAAAAGCTAAAATAAATAAA
Done.