Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 115 of 208
Found at i:34850431 original size:77 final size:76
Alignment explanation
Indices: 34850296--34850487 Score: 235
Period size: 77 Copynumber: 2.5 Consensus size: 76
34850286 GCTATTAGGA
* * *
34850296 GTACCGAAGTACAATAGGG-GCGTAAGTACGATCAGGGGTATCAAAGTACAACAAGGGCACGTAA
1 GTACCAAAGTACAATAGGGCACGTAAGTGCGATCA-GGGTATCAAAGTACAACAAGGGCACGTAA
34850360 GTACGATCAGGG
65 GTACGATCAGGG
* * * *
34850372 TTACTAAAGTACAATAGGGACACGTAAGTGCGATCAGGGTA-CTGAAGTACAACAGGGGCACGTA
1 GTACCAAAGTACAATAGGG-CACGTAAGTGCGATCAGGGTATC-AAAGTACAACAAGGGCACGTA
*
34850436 AGTGCGATCAGGG
64 AGTACGATCAGGG
* * *
34850449 GTACCGAAGTACAACAAGGGCACATAAGTGCGATCAGGG
1 GTACCAAAGTACAA-TAGGGCACGTAAGTGCGATCAGGG
34850488 GTATAGTTAT
Statistics
Matches: 99, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
76 17 0.17
77 65 0.66
78 17 0.17
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (76 bp):
GTACCAAAGTACAATAGGGCACGTAAGTGCGATCAGGGTATCAAAGTACAACAAGGGCACGTAAG
TACGATCAGGG
Found at i:34851390 original size:20 final size:20
Alignment explanation
Indices: 34851360--34851406 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
34851350 ACATAAGGGC
34851360 CTATATTTTATGGTTCCATAG
1 CTAT-TTTTATGGTTCCATAG
*
34851381 CTATTTTTATGTTTCCATAG
1 CTATTTTTATGGTTCCATAG
34851401 CTATTT
1 CTATTT
34851407 AATACCTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.53
Consensus pattern (20 bp):
CTATTTTTATGGTTCCATAG
Found at i:34855732 original size:20 final size:20
Alignment explanation
Indices: 34855707--34855768 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
34855697 CAAAGTACAA
*
34855707 CAGGGGCACGTAAGTGCGAT
1 CAGGGGCACATAAGTGCGAT
* * *
34855727 CAGGGGTACCA-AAGTAC-AA
1 CAGGGGCA-CATAAGTGCGAT
*
34855746 CAAGGGCACATAAGTGCGAT
1 CAGGGGCACATAAGTGCGAT
34855766 CAG
1 CAG
34855769 AGTACCAAAG
Statistics
Matches: 30, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
18 2 0.07
19 12 0.40
20 15 0.50
21 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.32, T:0.13
Consensus pattern (20 bp):
CAGGGGCACATAAGTGCGAT
Found at i:34855743 original size:77 final size:76
Alignment explanation
Indices: 34855618--34855847 Score: 309
Period size: 77 Copynumber: 3.0 Consensus size: 76
34855608 GTTCATCATT
* * ** * * * *
34855618 GTACCAGAGTACAATAGGGGCA-TAAGTGTAATCAGGGGTACCGAAGTACAATAGGGGCACATTA
1 GTACCAAAGTACAACAGGGGCAGTAAGTGCGATCAGGGGTACCAAAGTACAACAAGGGCACATAA
*
34855682 GTGTGATCAGG
66 GTGCGATCAGG
34855693 GTACCAAAGTACAACAGGGGCACGTAAGTGCGATCAGGGGTACCAAAGTACAACAAGGGCACATA
1 GTACCAAAGTACAACAGGGGCA-GTAAGTGCGATCAGGGGTACCAAAGTACAACAAGGGCACATA
*
34855758 AGTGCGATCAGA
65 AGTGCGATCAGG
* * *
34855770 GTACCAAAGTACAACAGAGGAATGTAAGTGCGATCAGGGGTACCAAAGTATAACAAGGGCACATA
1 GTACCAAAGTACAACAGGGGCA-GTAAGTGCGATCAGGGGTACCAAAGTACAACAAGGGCACATA
*
34855835 ACTGCGATCAGG
65 AGTGCGATCAGG
34855847 G
1 G
34855848 GTATAATTAT
Statistics
Matches: 137, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
75 20 0.15
77 117 0.85
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.16
Consensus pattern (76 bp):
GTACCAAAGTACAACAGGGGCAGTAAGTGCGATCAGGGGTACCAAAGTACAACAAGGGCACATAA
GTGCGATCAGG
Found at i:34855745 original size:39 final size:39
Alignment explanation
Indices: 34855618--34855850 Score: 276
Period size: 39 Copynumber: 6.1 Consensus size: 39
34855608 GTTCATCATT
* * **
34855618 GTACCAGAGTACAATAGGGG--CATAAGTGTAATCAGGG
1 GTACCAAAGTACAACAGGGGCACATAAGTGCGATCAGGG
* * * *
34855655 GTACCGAAGTACAATAGGGGCACATTAGTGTGATCA-GG
1 GTACCAAAGTACAACAGGGGCACATAAGTGCGATCAGGG
*
34855693 GTACCAAAGTACAACAGGGGCACGTAAGTGCGATCAGGG
1 GTACCAAAGTACAACAGGGGCACATAAGTGCGATCAGGG
* *
34855732 GTACCAAAGTACAACAAGGGCACATAAGTGCGATCA-GA
1 GTACCAAAGTACAACAGGGGCACATAAGTGCGATCAGGG
* * **
34855770 GTACCAAAGTACAACAGAGGAATGTAAGTGCGATCAGGG
1 GTACCAAAGTACAACAGGGGCACATAAGTGCGATCAGGG
* * *
34855809 GTACCAAAGTATAACAAGGGCACATAACTGCGATCAGGG
1 GTACCAAAGTACAACAGGGGCACATAAGTGCGATCAGGG
34855848 GTA
1 GTA
34855851 TAATTATATA
Statistics
Matches: 167, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
37 18 0.11
38 65 0.39
39 84 0.50
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.16
Consensus pattern (39 bp):
GTACCAAAGTACAACAGGGGCACATAAGTGCGATCAGGG
Found at i:34857397 original size:20 final size:20
Alignment explanation
Indices: 34857339--34857399 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
34857329 GTAGATGCGT
* * *
34857339 AACAGAGGCACCAAAGTGCA
1 AACAGAGGCATCGAAGTGTA
* *
34857359 TACAGAGGCAT-GATTGTGTA
1 AACAGAGGCATCGA-AGTGTA
34857379 AACAGAGGCATCGAAGTGTA
1 AACAGAGGCATCGAAGTGTA
34857399 A
1 A
34857400 TAGAGGCACC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 29 0.91
21 2 0.06
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.16
Consensus pattern (20 bp):
AACAGAGGCATCGAAGTGTA
Found at i:34857406 original size:19 final size:20
Alignment explanation
Indices: 34857382--34857435 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
34857372 TTGTGTAAAC
* *
34857382 AGAGGCATCGAAGTGT-AAT
1 AGAGGCACCAAAGTGTGAAT
34857401 AGAGGCACCAAAGTGTGAAT
1 AGAGGCACCAAAGTGTGAAT
* *
34857421 AGAAGCACAAAAGTG
1 AGAGGCACCAAAGTG
34857436 CAAACTCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.43, C:0.13, G:0.30, T:0.15
Consensus pattern (20 bp):
AGAGGCACCAAAGTGTGAAT
Found at i:34876411 original size:49 final size:50
Alignment explanation
Indices: 34876289--34876578 Score: 377
Period size: 50 Copynumber: 5.8 Consensus size: 50
34876279 TATAATAACA
* * ** * *
34876289 TGCCAAAGCCATGTCCCAGACATGGTGTTACATGGGAGTTTTTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
34876340 TGCCCATGCCATGTCCTAGACATGGTCTT-CAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* **
34876389 TGCCAACACCATGTCCTTGACATGGTCTTACATGGGACCTCTCA-CTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** **
34876438 TGCCAACGCCATGTCCCAGACATGGCCTTACATGAAACCTCTCATCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
34876488 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCAGCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
34876538 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
34876579 ATTACCCAAA
Statistics
Matches: 207, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
49 77 0.37
50 105 0.51
51 25 0.12
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:34887025 original size:15 final size:15
Alignment explanation
Indices: 34887005--34887038 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34886995 CGCAAACTTC
34887005 AAAAATAG-GGTAAGA
1 AAAAATAGTGGTAA-A
34887020 AAAAATAGTGGTAAA
1 AAAAATAGTGGTAAA
34887035 AAAA
1 AAAA
34887039 TTTCCTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (15 bp):
AAAAATAGTGGTAAA
Found at i:34892165 original size:56 final size:56
Alignment explanation
Indices: 34892098--34892212 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
34892088 AAAGAGTCTT
34892098 CAATCATATCTGAGAATATTGCCATAATACACCTTTAAAATGTGGTTAGTGCATTG
1 CAATCATATCTGAGAATATTGCCATAATACACCTTTAAAATGTGGTTAGTGCATTG
*
34892154 CAATCATATCTGAGAATATTGCCATAATACACCTTTAAAATGTGGTTGGTGCATTG
1 CAATCATATCTGAGAATATTGCCATAATACACCTTTAAAATGTGGTTAGTGCATTG
34892210 CAA
1 CAA
34892213 AGACTGAAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (56 bp):
CAATCATATCTGAGAATATTGCCATAATACACCTTTAAAATGTGGTTAGTGCATTG
Found at i:34903013 original size:23 final size:23
Alignment explanation
Indices: 34902972--34903017 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
34902962 TTTGTTATTT
34902972 TTTTTCTTTCGTTTCCCTCCTTTC
1 TTTTTCTTTCGTTTCCCT-CTTTC
* *
34902996 TTTTTC-TTCTTTTTCCTCTTTC
1 TTTTTCTTTCGTTTCCCTCTTTC
34903018 AAGTGAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTCTTTCGTTTCCCTCTTTC
Found at i:34906257 original size:18 final size:18
Alignment explanation
Indices: 34906222--34906264 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
34906212 CCATATCATT
*
34906222 AGCATAATATAAAACATA
1 AGCATAAAATAAAACATA
* *
34906240 AGCATAAAATCAACCATA
1 AGCATAAAATAAAACATA
*
34906258 ACCATAA
1 AGCATAA
34906265 GCTTGTCATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (18 bp):
AGCATAAAATAAAACATA
Found at i:34916568 original size:15 final size:15
Alignment explanation
Indices: 34916548--34916583 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
34916538 ATTTTGATAC
**
34916548 ATTTTGAAAATTTTT
1 ATTTTGAAAAAATTT
34916563 ATTTTGAAAAAATTT
1 ATTTTGAAAAAATTT
34916578 ATTTTG
1 ATTTTG
34916584 GGATATGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (15 bp):
ATTTTGAAAAAATTT
Found at i:34924359 original size:26 final size:26
Alignment explanation
Indices: 34924323--34924376 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
34924313 TAGCTTTAAA
34924323 GATGGTAAGTGATTTGAGCAAGAATT
1 GATGGTAAGTGATTTGAGCAAGAATT
34924349 GATGGTAAGTGATTTGAGCAAGAATT
1 GATGGTAAGTGATTTGAGCAAGAATT
34924375 GA
1 GA
34924377 ACTTTTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.30
Consensus pattern (26 bp):
GATGGTAAGTGATTTGAGCAAGAATT
Found at i:34928631 original size:25 final size:25
Alignment explanation
Indices: 34928583--34928696 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
34928573 GTACATTTAT
* * * *
34928583 GCTCATACGAGCTATGAATTGGTAT
1 GCTCATACGAGCTGTAAATCGGTAA
34928608 GCTC-TCACGAGCTGTAAATCGGTAA
1 GCTCAT-ACGAGCTGTAAATCGGTAA
* * *
34928633 GCTCATATGAGTTG-AGAATCGATAA
1 GCTCATACGAGCTGTA-AATCGGTAA
* **
34928658 GCTC-TCACGAGCT-AAAATTAGTAA
1 GCTCAT-ACGAGCTGTAAATCGGTAA
34928682 GCTCATACGAGCTGT
1 GCTCATACGAGCTGT
34928697 GATGTGTCCG
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
24 20 0.29
25 48 0.70
26 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTGTAAATCGGTAA
Found at i:34940862 original size:27 final size:27
Alignment explanation
Indices: 34940832--34940905 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
34940822 GTCCCAGTGA
* * *
34940832 ACTACCCTATGTTAACTGTCCTGATGG
1 ACTACCCTATGTTTACTGTCCCGACGG
* *
34940859 ACTACCCTATTTTTACTTTCCCGACGG
1 ACTACCCTATGTTTACTGTCCCGACGG
34940886 ACTA-CCTCATGTTTACTGTC
1 ACTACCCT-ATGTTTACTGTC
34940906 ATTAACTTCA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 3 0.08
27 36 0.92
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (27 bp):
ACTACCCTATGTTTACTGTCCCGACGG
Found at i:34958181 original size:27 final size:26
Alignment explanation
Indices: 34958143--34958427 Score: 295
Period size: 27 Copynumber: 10.7 Consensus size: 26
34958133 AGAGGTCAAT
* *
34958143 AAATGATCGAATTACCTCCACAGGGAA
1 AAATGACCGAATTACC-CCACAGGGTA
* *
34958170 AAATAACCGAATTACCCCTCAGGGT-
1 AAATGACCGAATTACCCCACAGGGTA
* *
34958195 -AATGACTGAATTACCCCCACAAGGTA
1 AAATGACCGAATTA-CCCCACAGGGTA
** *
34958221 AAATGACAAAATTACCCTAACAGGGTA
1 AAATGACCGAATTACCC-CACAGGGTA
*
34958248 AAATGACCGAATTACCCCCACAAGGTA
1 AAATGACCGAATTA-CCCCACAGGGTA
** *
34958275 AAATGAAAGAATTACCCTCGCAGGGTA
1 AAATGACCGAATTACCC-CACAGGGTA
* *
34958302 AAATGATCGAATTACCCCTATAGGGTA
1 AAATGACCGAATTACCCC-ACAGGGTA
**
34958329 AAATGACTAAATTACCCTCACAGGGTA
1 AAATGACCGAATTACCC-CACAGGGTA
**
34958356 AAATGACAAAATTACCCCTACAGGGTA
1 AAATGACCGAATTACCCC-ACAGGGTA
*
34958383 AAATGACCGAATTACCCCCACAGGATA
1 AAATGACCGAATTA-CCCCACAGGGTA
34958410 AAATGACCGAATTACCCC
1 AAATGACCGAATTACCCC
34958428 TAGGAGATGA
Statistics
Matches: 216, Mismatches: 32, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
24 11 0.05
25 9 0.04
26 19 0.09
27 169 0.78
28 8 0.04
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (26 bp):
AAATGACCGAATTACCCCACAGGGTA
Found at i:34958428 original size:54 final size:54
Alignment explanation
Indices: 34958143--34958429 Score: 332
Period size: 54 Copynumber: 5.4 Consensus size: 54
34958133 AGAGGTCAAT
* * * * *
34958143 AAATGATCGAATTACCTCC-ACAGGGAAAAATAACCGAATTACCC-CTCAGGGT-
1 AAATGACCGAATTACC-CCTACAGGGTAAAATGACAGAATTACCCTCACAGGGTA
* * * * *
34958195 -AATGACTGAATTACCCCCACAAGGTAAAATGACAAAATTACCCTAACAGGGTA
1 AAATGACCGAATTACCCCTACAGGGTAAAATGACAGAATTACCCTCACAGGGTA
* * * *
34958248 AAATGACCGAATTACCCCCACAAGGTAAAATGAAAGAATTACCCTCGCAGGGTA
1 AAATGACCGAATTACCCCTACAGGGTAAAATGACAGAATTACCCTCACAGGGTA
* *
34958302 AAATGATCGAATTACCCCTATAGGGTAAAATGACTA-AATTACCCTCACAGGGTA
1 AAATGACCGAATTACCCCTACAGGGTAAAATGAC-AGAATTACCCTCACAGGGTA
** * * *
34958356 AAATGACAAAATTACCCCTACAGGGTAAAATGACCGAATTACCCCCACAGGATA
1 AAATGACCGAATTACCCCTACAGGGTAAAATGACAGAATTACCCTCACAGGGTA
34958410 AAATGACCGAATTACCCCTA
1 AAATGACCGAATTACCCCTA
34958430 GGAGATGAAA
Statistics
Matches: 200, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.01
51 33 0.17
52 6 0.03
54 158 0.79
55 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (54 bp):
AAATGACCGAATTACCCCTACAGGGTAAAATGACAGAATTACCCTCACAGGGTA
Found at i:34959016 original size:10 final size:10
Alignment explanation
Indices: 34959003--34959037 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
34958993 GGAGGTTCTA
34959003 CATTTGCTTT
1 CATTTGCTTT
*
34959013 CATTTACTTT
1 CATTTGCTTT
34959023 CATTTGCTTT
1 CATTTGCTTT
34959033 CATTT
1 CATTT
34959038 AAATTTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.14, C:0.20, G:0.06, T:0.60
Consensus pattern (10 bp):
CATTTGCTTT
Found at i:34974376 original size:19 final size:21
Alignment explanation
Indices: 34974338--34974377 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
34974328 CAGTGTTAAG
34974338 AAACATTCAAACACCAAGATT
1 AAACATTCAAACACCAAGATT
*
34974359 AAACATT-AAA-AGCAAGATT
1 AAACATTCAAACACCAAGATT
34974378 GAATAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACATTCAAACACCAAGATT
Found at i:34975117 original size:21 final size:20
Alignment explanation
Indices: 34975092--34975135 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
34975082 CCGCAAAAAC
34975092 ATTTTATCTTGTCTATTTACT
1 ATTTTATCTTGTCTATTTA-T
* *
34975113 ATTTTATTTTGTTTATTTAT
1 ATTTTATCTTGTCTATTTAT
34975133 ATT
1 ATT
34975136 AATTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (20 bp):
ATTTTATCTTGTCTATTTAT
Found at i:34978156 original size:11 final size:11
Alignment explanation
Indices: 34978140--34978165 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
34978130 GTTCCAATGC
34978140 ATTTGTTTGCT
1 ATTTGTTTGCT
34978151 ATTTGTTTGCT
1 ATTTGTTTGCT
34978162 ATTT
1 ATTT
34978166 CCCCGTTCAT
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:0.12, C:0.08, G:0.15, T:0.65
Consensus pattern (11 bp):
ATTTGTTTGCT
Found at i:34978770 original size:14 final size:13
Alignment explanation
Indices: 34978738--34978772 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
34978728 TTAATGTATT
34978738 ATTTTAAATTCTA
1 ATTTTAAATTCTA
*
34978751 AATTTAAATTCTA
1 ATTTTAAATTCTA
34978764 AGTTTTAAA
1 A-TTTTAAA
34978773 GTTAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (13 bp):
ATTTTAAATTCTA
Found at i:34978948 original size:43 final size:43
Alignment explanation
Indices: 34978895--34979027 Score: 191
Period size: 43 Copynumber: 3.1 Consensus size: 43
34978885 AGATATGTTT
* *
34978895 TAGCGACGTTTGTGGTAAAAGCGCCGCTAAAGGT-CTTGATCTA
1 TAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCCTAG-TCTA
*
34978938 TAGCGGCGTTTGT-GTGAAAAGCGCCGCTAAAGGTCCTAGTGTA
1 TAGCGGCGTTTGTGGT-AAAAGCGCCGCTAAAGGTCCTAGTCTA
34978981 TAGCGGCGTTTGTGCG-AAAAGCGCCGCTAAAGGTCCTAGTCTA
1 TAGCGGCGTTTGTG-GTAAAAGCGCCGCTAAAGGTCCTAGTCTA
34979024 TAGC
1 TAGC
34979028 CGCTAAAGGT
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
42 2 0.02
43 76 0.93
44 3 0.04
45 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCCTAGTCTA
Found at i:34979033 original size:23 final size:23
Alignment explanation
Indices: 34979003--34979050 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
34978993 TGCGAAAAGC
34979003 GCCGCTAAAGGTCCT-AGTCTATA
1 GCCGCTAAAGGTCCTGA-TCTATA
34979026 GCCGCTAAAGGTCCTGATCTATA
1 GCCGCTAAAGGTCCTGATCTATA
34979049 GC
1 GC
34979051 GGCGTTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (23 bp):
GCCGCTAAAGGTCCTGATCTATA
Found at i:34979067 original size:66 final size:66
Alignment explanation
Indices: 34978960--34979093 Score: 234
Period size: 66 Copynumber: 2.0 Consensus size: 66
34978950 TGTGAAAAGC
* *
34978960 GCCGCTAAAGGTCCTAGTGTATAGCGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTCCTAGTCTAT
1 GCCGCTAAAGGTCCTAGTCTATAGCGGCGTTTGTGCAAAAAGCGCCGCTAAAGGTCCTAGTCTAT
34979025 A
66 A
34979026 GCCGCTAAAGGTCCT-GATCTATAGCGGCGTTTGTGCAAAAAGCGCCGCTAAAGGTCCTAGTCTA
1 GCCGCTAAAGGTCCTAG-TCTATAGCGGCGTTTGTGCAAAAAGCGCCGCTAAAGGTCCTAGTCTA
34979090 TA
65 TA
34979092 GC
1 GC
34979094 GGCGTTTGTA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 1 0.02
66 64 0.98
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (66 bp):
GCCGCTAAAGGTCCTAGTCTATAGCGGCGTTTGTGCAAAAAGCGCCGCTAAAGGTCCTAGTCTAT
A
Found at i:34979090 original size:43 final size:43
Alignment explanation
Indices: 34979026--34979143 Score: 184
Period size: 43 Copynumber: 2.7 Consensus size: 43
34979016 CTAGTCTATA
*
34979026 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGCAAAAAGC
1 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTACAAAAAGC
*
34979069 GCCGCTAAAGGTCCT-AGTCTATAGCGGCGTTTGTACGAAAAGC
1 GCCGCTAAAGGTCCTGA-TCTATAGCGGCGTTTGTACAAAAAGC
* *
34979112 ACCGCTAAAGGTCTTGATCTATAGCGGCGTTT
1 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTT
34979144 ATCTAACGCC
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
42 1 0.01
43 67 0.97
44 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (43 bp):
GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTACAAAAAGC
Found at i:34979136 original size:109 final size:109
Alignment explanation
Indices: 34978917--34979124 Score: 362
Period size: 109 Copynumber: 1.9 Consensus size: 109
34978907 TGGTAAAAGC
* ** *
34978917 GCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCCTAGTGTAT
1 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGCAAAAAGCGCCGCTAAAGGTCCTAGTCTAT
* *
34978982 AGCGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTCCTAGTCTATA
66 AGCGGCGTTTGTACGAAAAGCACCGCTAAAGGTCCTAGTCTATA
34979026 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGCAAAAAGCGCCGCTAAAGGTCCTAGTCTAT
1 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGCAAAAAGCGCCGCTAAAGGTCCTAGTCTAT
34979091 AGCGGCGTTTGTACGAAAAGCACCGCTAAAGGTC
66 AGCGGCGTTTGTACGAAAAGCACCGCTAAAGGTC
34979125 TTGATCTATA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 93 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (109 bp):
GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGCAAAAAGCGCCGCTAAAGGTCCTAGTCTAT
AGCGGCGTTTGTACGAAAAGCACCGCTAAAGGTCCTAGTCTATA
Found at i:34980388 original size:59 final size:59
Alignment explanation
Indices: 34980296--34980419 Score: 196
Period size: 59 Copynumber: 2.1 Consensus size: 59
34980286 GTGAATTGAA
* * *
34980296 AAATCCTTGGTGGTGGAAAGCTAAGATAGTGGAAATAGGCAATTGA-AGCAAACCACTAT
1 AAATCATTGGTCGTGGAAAGCTAAGATAGTGGAAATAGACAATTGAGA-CAAACCACTAT
*
34980355 AAATCATTGGTCGTGGAAAGCTAAGATAGTGGAAATAGACAATTGAGACGAACCACTAT
1 AAATCATTGGTCGTGGAAAGCTAAGATAGTGGAAATAGACAATTGAGACAAACCACTAT
34980414 AAATCA
1 AAATCA
34980420 AAGTGTACAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
59 59 0.98
60 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (59 bp):
AAATCATTGGTCGTGGAAAGCTAAGATAGTGGAAATAGACAATTGAGACAAACCACTAT
Found at i:34980854 original size:17 final size:19
Alignment explanation
Indices: 34980821--34980855 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
34980811 TTGGCATTGT
34980821 TATAAAGAAATTAATTAAC
1 TATAAAGAAATTAATTAAC
34980840 TATAAA-AAA-TAATTAA
1 TATAAAGAAATTAATTAA
34980856 AAAATATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
TATAAAGAAATTAATTAAC
Found at i:34980978 original size:18 final size:19
Alignment explanation
Indices: 34980941--34980978 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
34980931 AAATGTTTGT
*
34980941 AATAATTTCATAAAAATCA
1 AATAATTTCAGAAAAATCA
*
34980960 AATAATTT-AGAAAATTCA
1 AATAATTTCAGAAAAATCA
34980978 A
1 A
34980979 TGCAAACACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (19 bp):
AATAATTTCAGAAAAATCA
Found at i:34981090 original size:15 final size:15
Alignment explanation
Indices: 34981057--34981102 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
34981047 TTACAAAATT
*
34981057 TTAATTTTA-TAACA
1 TTAATTTTATTAAAA
34981071 TTAATTTTATTAAAA
1 TTAATTTTATTAAAA
*
34981086 TTAATATTATATAAAA
1 TTAATTTTAT-TAAAA
34981102 T
1 T
34981103 ATTATGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 9 0.32
15 13 0.46
16 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATTTTATTAAAA
Found at i:34985949 original size:21 final size:21
Alignment explanation
Indices: 34985902--34985956 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
34985892 TGGTTATTAT
*
34985902 ACACCTATAACTACATTTAAA
1 ACACCTATAACAACATTTAAA
* * *
34985923 ATACCTATAACAACATTTGAG
1 ACACCTATAACAACATTTAAA
*
34985944 ACACCTAAAACAA
1 ACACCTATAACAA
34985957 TAATTGAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.24
Consensus pattern (21 bp):
ACACCTATAACAACATTTAAA
Found at i:34985963 original size:21 final size:21
Alignment explanation
Indices: 34985925--34985964 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
34985915 CATTTAAAAT
* *
34985925 ACCTATAACAACATTTGAGAC
1 ACCTAAAACAACAATTGAGAC
*
34985946 ACCTAAAACAATAATTGAG
1 ACCTAAAACAACAATTGAG
34985965 GTTGAAATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (21 bp):
ACCTAAAACAACAATTGAGAC
Found at i:34990908 original size:58 final size:57
Alignment explanation
Indices: 34990835--34990951 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 57
34990825 AATAATTACT
* * * **
34990835 AAGTTTAGGCACCAATGTGAGAATAATTACTAAATTCAGGGTTTAACTTGGGCCAAAA
1 AAGTTTAAGCACCAATGTGAGAACAATTACCAAATTCAGGACTTAACTT-GGCCAAAA
* * *
34990893 AAGTTTAAGCTCCAATGTGAGAACAATTGCCAAGTTCAGGACTTAACTTGGCCAAAA
1 AAGTTTAAGCACCAATGTGAGAACAATTACCAAATTCAGGACTTAACTTGGCCAAAA
34990950 AA
1 AA
34990952 AAGTTCAAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 10 0.20
58 41 0.80
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (57 bp):
AAGTTTAAGCACCAATGTGAGAACAATTACCAAATTCAGGACTTAACTTGGCCAAAA
Found at i:34990952 original size:58 final size:59
Alignment explanation
Indices: 34990835--34990971 Score: 152
Period size: 58 Copynumber: 2.3 Consensus size: 59
34990825 AATAATTACT
* * * **
34990835 AAGTTTAGGCACCAATGTGAGAATAATTACTAAATTCAGGGTTTAACTTGGGCC-AAAA
1 AAGTTTAAGCACCAATGTGAGAACAATTACCAAATTCAGGACTTAACTTGGGCCAAAAA
* * *
34990893 AAGTTTAAGCTCCAATGTGAGAACAATTGCCAAGTTCAGGACTTAACTT-GGCCAAAAAA
1 AAGTTTAAGCACCAATGTGAGAACAATTACCAAATTCAGGACTTAACTTGGGCC-AAAAA
* * *
34990952 AAGTTCAAACCCCAATGTGA
1 AAGTTTAAGCACCAATGTGA
34990972 AAAAAATTTA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
57 4 0.06
58 41 0.62
59 21 0.32
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (59 bp):
AAGTTTAAGCACCAATGTGAGAACAATTACCAAATTCAGGACTTAACTTGGGCCAAAAA
Found at i:34993313 original size:22 final size:22
Alignment explanation
Indices: 34993256--34993313 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
34993246 AACTAGCCTC
*
34993256 AACCAAAAATGAGACCAACCCAA
1 AACC-AAAATGAAACCAACCCAA
* * *
34993279 AACGAAAAAGAAACCGACCC-A
1 AACCAAAATGAAACCAACCCAA
34993300 AACCAAAATTGAAA
1 AACCAAAA-TGAAA
34993314 ATTGTCCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 8 0.29
22 17 0.61
23 3 0.11
ACGTcount: A:0.59, C:0.26, G:0.10, T:0.05
Consensus pattern (22 bp):
AACCAAAATGAAACCAACCCAA
Found at i:35005641 original size:31 final size:32
Alignment explanation
Indices: 35005603--35005663 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
35005593 CATCGTTAAT
35005603 CCAACC-A-AAACACACCATATGCTCATAAAAG
1 CCAACCAACAAACACACCA-ATGCTCATAAAAG
35005634 CCAACCAAACAAACACACCAATGCTCATAA
1 CCAACC-AACAAACACACCAATGCTCATAA
35005664 GAGCTTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 6 0.22
33 11 0.41
34 10 0.37
ACGTcount: A:0.49, C:0.34, G:0.05, T:0.11
Consensus pattern (32 bp):
CCAACCAACAAACACACCAATGCTCATAAAAG
Found at i:35005760 original size:35 final size:34
Alignment explanation
Indices: 35005601--35005759 Score: 133
Period size: 35 Copynumber: 4.6 Consensus size: 34
35005591 TACATCGTTA
* * *
35005601 ATCCAACCAAAACACACCATATGCTCATAAAAGCC
1 ATCCAACCGAAACACACCA-ATGCTCATAAGAGCT
* *
35005636 AACCAAAC-AAACACACCAATGCTCATAAGAGCTT
1 ATCCAACCGAAACACACCAATGCTCATAAGAGC-T
* ** * **
35005670 ATCTCTA-CGAAACACAAGAATGGTCATAAGATTT
1 ATC-CAACCGAAACACACCAATGCTCATAAGAGCT
** *
35005704 AGTCCAACCGAAACATGCCAAAGCTCATAAGAGCT
1 A-TCCAACCGAAACACACCAATGCTCATAAGAGCT
35005739 AGTCCAACCGAAACACACCAA
1 A-TCCAACCGAAACACACCAA
35005760 ATAGTATGTA
Statistics
Matches: 97, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
33 13 0.13
34 17 0.18
35 67 0.69
ACGTcount: A:0.44, C:0.29, G:0.11, T:0.16
Consensus pattern (34 bp):
ATCCAACCGAAACACACCAATGCTCATAAGAGCT
Found at i:35006692 original size:18 final size:18
Alignment explanation
Indices: 35006669--35006703 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
35006659 GTATGGAAAG
35006669 TAAAATGAAGAAGAAACT
1 TAAAATGAAGAAGAAACT
35006687 TAAAATGAAGAAGAAAC
1 TAAAATGAAGAAGAAAC
35006704 GTTTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.17, T:0.14
Consensus pattern (18 bp):
TAAAATGAAGAAGAAACT
Found at i:35017380 original size:10 final size:10
Alignment explanation
Indices: 35017365--35017389 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35017355 ATGAATTATG
35017365 AATTAATTGA
1 AATTAATTGA
35017375 AATTAATTGA
1 AATTAATTGA
35017385 AATTA
1 AATTA
35017390 TCTATTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (10 bp):
AATTAATTGA
Found at i:35019752 original size:12 final size:12
Alignment explanation
Indices: 35019735--35019760 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35019725 TTGAAGTACT
35019735 TGTAATTGGACC
1 TGTAATTGGACC
35019747 TGTAATTGGACC
1 TGTAATTGGACC
35019759 TG
1 TG
35019761 ATATGAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (12 bp):
TGTAATTGGACC
Found at i:35031375 original size:46 final size:46
Alignment explanation
Indices: 35031308--35031469 Score: 276
Period size: 46 Copynumber: 3.6 Consensus size: 46
35031298 TTTGAGTACT
35031308 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
35031354 TCTGATCAAGTGGCAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
35031400 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
35031445 TCTGATC-AGAGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
35031470 ATCATATGTA
Statistics
Matches: 112, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
43 12 0.11
44 5 0.04
45 19 0.17
46 76 0.68
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:35050549 original size:50 final size:50
Alignment explanation
Indices: 35050442--35050689 Score: 298
Period size: 50 Copynumber: 4.8 Consensus size: 50
35050432 ATTTGGGTAA
* *
35050442 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
35050498 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
35050548 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
35050598 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
35050648 AGAACTCTCATGTAAGACCATATCTAGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
35050690 GTACAAGAAA
Statistics
Matches: 173, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
50 128 0.74
53 3 0.02
55 1 0.01
56 41 0.24
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:35054958 original size:29 final size:29
Alignment explanation
Indices: 35054916--35054971 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
35054906 AAAAGTCATT
35054916 TTTTTTCAATATTTACCGAAATGGGCCGG
1 TTTTTTCAATATTTACCGAAATGGGCCGG
*
35054945 TTTTTT-AATTATTTACCGGAATGGGCC
1 TTTTTTCAA-TATTTACCGAAATGGGCC
35054972 ATTTTCCACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (29 bp):
TTTTTTCAATATTTACCGAAATGGGCCGG
Found at i:35057817 original size:31 final size:30
Alignment explanation
Indices: 35057779--35057877 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 30
35057769 TTAACATACG
35057779 ATTTGATACTTGAATTTAACTTTAATATTTA
1 ATTTGATACTTGAATTT-ACTTTAATATTTA
* * * *
35057810 ATTTGATATTTGAGTTT--TTT-TTGTTTA
1 ATTTGATACTTGAATTTACTTTAATATTTA
* * * *
35057837 ATATGGTACTTGAATTTGACTCTAATATTCA
1 ATTTGATACTTGAATTT-ACTTTAATATTTA
35057868 ATTTGATACT
1 ATTTGATACT
35057878 CAAAGTAAAT
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
27 18 0.36
28 3 0.06
30 2 0.04
31 27 0.54
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (30 bp):
ATTTGATACTTGAATTTACTTTAATATTTA
Found at i:35058118 original size:18 final size:18
Alignment explanation
Indices: 35058095--35058129 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35058085 AGATAAAAAA
35058095 AAATTTAAATATCAAATT
1 AAATTTAAATATCAAATT
**
35058113 AAATTTCGATATCAAAT
1 AAATTTAAATATCAAAT
35058130 AATATATTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (18 bp):
AAATTTAAATATCAAATT
Found at i:35060974 original size:13 final size:13
Alignment explanation
Indices: 35060953--35061001 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
35060943 GTTTAATTAG
*
35060953 ATTTTTAATAAAT
1 ATTTATAATAAAT
* *
35060966 ATTTATAATTATAG
1 ATTTATAA-TAAAT
*
35060980 ATTTTTAATAAAT
1 ATTTATAATAAAT
35060993 ATTTATAAT
1 ATTTATAAT
35061002 TATAGATTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
ATTTATAATAAAT
Found at i:35060980 original size:27 final size:27
Alignment explanation
Indices: 35060950--35061011 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
35060940 AAGGTTTAAT
35060950 TAGATTTTTAATAAATATTTATAATTA
1 TAGATTTTTAATAAATATTTATAATTA
35060977 TAGATTTTTAATAAATATTTATAATTA
1 TAGATTTTTAATAAATATTTATAATTA
35061004 TAGATTTT
1 TAGATTTT
35061012 ATAAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (27 bp):
TAGATTTTTAATAAATATTTATAATTA
Found at i:35061024 original size:14 final size:13
Alignment explanation
Indices: 35060946--35061026 Score: 62
Period size: 14 Copynumber: 6.0 Consensus size: 13
35060936 AATTAAGGTT
*
35060946 TAATTAGATTTT-
1 TAATTAAATTTTA
35060958 TAA-TAAATATTTA
1 TAATTAAAT-TTTA
35060971 TAATTATAGATTTT-
1 TAATTA-A-ATTTTA
35060985 TAA-TAAATATTTA
1 TAATTAAAT-TTTA
35060998 TAATTATAGATTTTA
1 TAATTA-A-ATTTTA
35061013 TAAATTAAATTTTA
1 T-AATTAAATTTTA
35061027 GATAAATATA
Statistics
Matches: 57, Mismatches: 1, Indels: 20
0.73 0.01 0.26
Matches are distributed among these distances:
11 6 0.11
12 10 0.18
13 8 0.14
14 13 0.23
15 11 0.19
16 9 0.16
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (13 bp):
TAATTAAATTTTA
Found at i:35061112 original size:19 final size:19
Alignment explanation
Indices: 35061088--35061153 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
35061078 AAACCTAAAA
35061088 TAAAATAATTTTATCTAAT
1 TAAAATAATTTTATCTAAT
***
35061107 TAAAATTAA-AAAATCTAAAT
1 TAAAA-TAATTTTATCT-AAT
*
35061127 TCAAAAATAATTTTATCTAAA
1 T--AAAATAATTTTATCTAAT
35061148 TAAAAT
1 TAAAAT
35061154 CTAAAATCTC
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 14 0.40
20 7 0.20
21 6 0.17
22 8 0.23
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATAATTTTATCTAAT
Found at i:35061141 original size:41 final size:43
Alignment explanation
Indices: 35061089--35061195 Score: 128
Period size: 41 Copynumber: 2.5 Consensus size: 43
35061079 AACCTAAAAT
* *
35061089 AAAATAATTTTATCTAATTAAAAT-TAAAAAATCTAAATTC-A
1 AAAATAATTTTATCTAATTAAAATCTAAAAAATCAAAACTCAA
* **
35061130 AAAATAATTTTATCTAAATAAAATCTAAAATCTCAAAACTCAA
1 AAAATAATTTTATCTAATTAAAATCTAAAAAATCAAAACTCAA
* *
35061173 AAACAAAATTTTATGTAATTAAA
1 AAA-ATAATTTTATCTAATTAAA
35061196 GGGTATATCA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 23 0.42
42 12 0.22
43 4 0.07
44 16 0.29
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (43 bp):
AAAATAATTTTATCTAATTAAAATCTAAAAAATCAAAACTCAA
Found at i:35064611 original size:2 final size:2
Alignment explanation
Indices: 35064604--35064635 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
35064594 GTCGATGTTT
35064604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35064636 TCACGTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35068232 original size:28 final size:30
Alignment explanation
Indices: 35068201--35068264 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
35068191 ATCAAAACTT
35068201 TATTTTAAAAATA-AAAAAATAAAAA-AAA
1 TATTTTAAAAATATAAAAAATAAAAATAAA
**
35068229 TATTTTAAAAATATTTTAAAATAAAAATAAA
1 TATTTTAAAAATA-TAAAAAATAAAAATAAA
35068260 TATTT
1 TATTT
35068265 ATTATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 13 0.42
30 10 0.32
31 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
TATTTTAAAAATATAAAAAATAAAAATAAA
Found at i:35068251 original size:10 final size:11
Alignment explanation
Indices: 35068224--35068249 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35068214 AAAAAATAAA
35068224 AAAAATATTTT
1 AAAAATATTTT
35068235 AAAAATATTTT
1 AAAAATATTTT
35068246 AAAA
1 AAAA
35068250 TAAAAATAAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:35070990 original size:38 final size:38
Alignment explanation
Indices: 35070948--35071025 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
35070938 CGTCACATCA
*
35070948 ATAAAATTATTAGAGAACTTCCTTAAACATACTTGTAG
1 ATAAAATTATTAGAGAACTTCCTCAAACATACTTGTAG
35070986 ATAAAATTATTAGAGAACTTCCTCAAACATACTTGTAG
1 ATAAAATTATTAGAGAACTTCCTCAAACATACTTGTAG
35071024 AT
1 AT
35071026 CATCTTTCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (38 bp):
ATAAAATTATTAGAGAACTTCCTCAAACATACTTGTAG
Found at i:35077256 original size:18 final size:17
Alignment explanation
Indices: 35077234--35077292 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
35077224 GGAGGCTCAA
35077234 GTGAGGAAGAAGATGTAG
1 GTGAGGAA-AAGATGTAG
* *
35077252 ATGA-G-AAAGATGTTG
1 GTGAGGAAAAGATGTAG
*
35077267 GGGAGGAAAACGATGTAG
1 GTGAGGAAAA-GATGTAG
35077285 GTGAGGAA
1 GTGAGGAA
35077293 GAAGGGGTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 10 0.31
16 2 0.06
17 4 0.12
18 16 0.50
ACGTcount: A:0.39, C:0.02, G:0.42, T:0.17
Consensus pattern (17 bp):
GTGAGGAAAAGATGTAG
Found at i:35077946 original size:29 final size:29
Alignment explanation
Indices: 35077913--35077981 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
35077903 GGCTGTACGA
* * *
35077913 ACAGCCCGTGTGTGATACAC-AGCCGTGTG
1 ACAGCCCGTGTGTGACACACGA-CCATATG
35077942 ACAGCCCGTGTGTGACACACGACCATATG
1 ACAGCCCGTGTGTGACACACGACCATATG
35077971 ACAGCCCGTGT
1 ACAGCCCGTGT
35077982 TTTAGGCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (29 bp):
ACAGCCCGTGTGTGACACACGACCATATG
Found at i:35081886 original size:21 final size:21
Alignment explanation
Indices: 35081861--35081901 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
35081851 GCATTTTTTA
35081861 TTAAC-TAATAAAACACATATT
1 TTAACATAATAAAACA-ATATT
35081882 TTAACATAATAAAACAATAT
1 TTAACATAATAAAACAATAT
35081902 CCACTGTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAACATAATAAAACAATATT
Found at i:35093255 original size:17 final size:18
Alignment explanation
Indices: 35093222--35093255 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35093212 TGTTAACACT
*
35093222 TAAAATAATATTATATAG
1 TAAAATAATAGTATATAG
35093240 TAAAATAAT-GTATATA
1 TAAAATAATAGTATATA
35093256 AAAAAATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAAATAATAGTATATAG
Found at i:35096961 original size:27 final size:28
Alignment explanation
Indices: 35096909--35096970 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
35096899 ATCTCTCTAT
*** *
35096909 AAAAATGGCTTATTTCCCTAATTTTTGA
1 AAAAATGGCTTAAAACCCTAATTTTTAA
35096937 AAAAATGGCTTAAAACCCTAA-TTTTAA
1 AAAAATGGCTTAAAACCCTAATTTTTAA
35096964 AAAAATG
1 AAAAATG
35096971 ACATATACCG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (28 bp):
AAAAATGGCTTAAAACCCTAATTTTTAA
Found at i:35098047 original size:22 final size:21
Alignment explanation
Indices: 35098003--35098044 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35097993 ACATACATAA
*
35098003 ATTTTTTAAAAGTACAAATTT
1 ATTTTTTAAAAGTAAAAATTT
*
35098024 ATTTTTTGAAAGTAAAAATTT
1 ATTTTTTAAAAGTAAAAATTT
35098045 TATCCTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (21 bp):
ATTTTTTAAAAGTAAAAATTT
Found at i:35102121 original size:8 final size:8
Alignment explanation
Indices: 35102108--35102135 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
35102098 GGATTCAAAG
35102108 AAAGAAAT
1 AAAGAAAT
35102116 AAAGAAAT
1 AAAGAAAT
35102124 AAAGAAAT
1 AAAGAAAT
35102132 AAAG
1 AAAG
35102136 GTTTGTCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (8 bp):
AAAGAAAT
Found at i:35107912 original size:42 final size:42
Alignment explanation
Indices: 35107858--35107937 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
35107848 CTATAAAACC
*
35107858 AAGAATTTAAAAAGAGGAGAAGATA-ATATTGGGTTGTTAAAA
1 AAGAATTTAAAAAGAGGAGAAGATAGA-AATGGGTTGTTAAAA
35107900 AAGAATTTAAAAAGAGGAGAAGATAGAAATGGGTTGTT
1 AAGAATTTAAAAAGAGGAGAAGATAGAAATGGGTTGTT
35107938 GGTTTTACCC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.25
Consensus pattern (42 bp):
AAGAATTTAAAAAGAGGAGAAGATAGAAATGGGTTGTTAAAA
Found at i:35108041 original size:13 final size:13
Alignment explanation
Indices: 35108023--35108048 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35108013 CATAGGCAAA
35108023 ATTAGAGGGTAGT
1 ATTAGAGGGTAGT
35108036 ATTAGAGGGTAGT
1 ATTAGAGGGTAGT
35108049 GATTGAGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (13 bp):
ATTAGAGGGTAGT
Found at i:35114854 original size:9 final size:10
Alignment explanation
Indices: 35114809--35114855 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
35114799 TAACATGTTG
*
35114809 AATTTTAATT
1 AATTTTTATT
*
35114819 AATTTTATATCA
1 AATTTT-TAT-T
35114831 AATTTTTATT
1 AATTTTTATT
35114841 AATTTTTATT
1 AATTTTTATT
35114851 -ATTTT
1 AATTTT
35114856 CGACAGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 5 0.16
10 16 0.50
11 5 0.16
12 6 0.19
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
AATTTTTATT
Found at i:35115007 original size:22 final size:22
Alignment explanation
Indices: 35114982--35115026 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
35114972 ATTTTTTGTA
35114982 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
*
35115004 TTAATTATAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
35115026 T
1 T
35115027 GGGTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:35115012 original size:16 final size:16
Alignment explanation
Indices: 35114993--35115025 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35114983 TAATTCATAA
35114993 TATAAT-TAATTTTAAT
1 TATAATCTAA-TTTAAT
35115009 TATAATCTAATTTAAT
1 TATAATCTAATTTAAT
35115025 T
1 T
35115026 TGGGTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAATCTAATTTAAT
Found at i:35123812 original size:43 final size:43
Alignment explanation
Indices: 35123721--35123955 Score: 209
Period size: 41 Copynumber: 5.6 Consensus size: 43
35123711 ATGGATCCCG
* * * *
35123721 GTGGAATTAGCACTTAGCAACCACC-TT-ATAATCAATGATAC
1 GTGGAATCAGCACATAGAAACCACCTTTCACAATCAATGATAC
* * *
35123762 GGGGAATCAGCACATAGAAACC-CCTTTCACAATCAAGGATAT
1 GTGGAATCAGCACATAGAAACCACCTTTCACAATCAATGATAC
* * *
35123804 GATGGAATCAGCACTTAGCAACCACC-TT-ATAATCAATGATAC
1 G-TGGAATCAGCACATAGAAACCACCTTTCACAATCAATGATAC
* * *
35123846 GGGGAATCGGCACATAGCAACC-CCTTTCACAATCAATGATAC
1 GTGGAATCAGCACATAGAAACCACCTTTCACAATCAATGATAC
* * *
35123888 GGTGGAATCAGCACTTAGAAACCACC-TT-ATAATCAATGACAC
1 -GTGGAATCAGCACATAGAAACCACCTTTCACAATCAATGATAC
* * * *
35123930 GGGGAATCTGCACTTAGCAACC-CCTT
1 GTGGAATCAGCACATAGAAACCACCTT
35123956 ACATTCAAAG
Statistics
Matches: 159, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
40 6 0.04
41 60 0.38
42 49 0.31
43 40 0.25
44 4 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (43 bp):
GTGGAATCAGCACATAGAAACCACCTTTCACAATCAATGATAC
Found at i:35123825 original size:84 final size:84
Alignment explanation
Indices: 35123722--35123955 Score: 378
Period size: 84 Copynumber: 2.8 Consensus size: 84
35123712 TGGATCCCGG
* *
35123722 TGGAATTAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGAAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
*
35123787 TTCACAATCAAGGATATGA
66 TTCACAATCAAGGATACGA
*
35123806 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCGGCACATAGCAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
* *
35123871 TTCACAATCAATGATACGG
66 TTCACAATCAAGGATACGA
* * * *
35123890 TGGAATCAGCACTTAGAAACCACCTTATAATCAATGACACGGGGAATCTGCACTTAGCAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
35123955 T
66 T
35123956 ACATTCAAAG
Statistics
Matches: 140, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 140 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (84 bp):
TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
TTCACAATCAAGGATACGA
Found at i:35127630 original size:9 final size:9
Alignment explanation
Indices: 35127588--35127676 Score: 58
Period size: 9 Copynumber: 9.9 Consensus size: 9
35127578 ATAATTTTTT
35127588 TAAAAATATA
1 TAAAAATA-A
35127598 TTAAAAATAGA
1 -TAAAAATA-A
* * *
35127609 AAAAAACAT
1 TAAAAATAA
35127618 TAAAAATAA
1 TAAAAATAA
35127627 TAAAAAT--
1 TAAAAATAA
* *
35127634 TGAAAATTA
1 TAAAAATAA
* *
35127643 TTAAAATTA
1 TAAAAATAA
*
35127652 TTAAAATAA
1 TAAAAATAA
35127661 TAAAAAT-A
1 TAAAAATAA
35127669 TAAAAATA
1 TAAAAATA
35127677 TAGAAATTCT
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
7 6 0.09
8 8 0.12
9 35 0.55
10 6 0.09
11 9 0.14
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (9 bp):
TAAAAATAA
Found at i:35127639 original size:17 final size:16
Alignment explanation
Indices: 35127597--35127676 Score: 70
Period size: 16 Copynumber: 4.6 Consensus size: 16
35127587 TTAAAAATAT
*
35127597 ATTAAAAATAGAAAAAAA
1 ATTAAAAAT--AATAAAA
35127615 CATTAAAAATAATAAAA
1 -ATTAAAAATAATAAAA
* * *
35127632 ATTGAAAATTATTAAA
1 ATTAAAAATAATAAAA
35127648 ATTATTAAAATAATAAAA
1 ATTA--AAAATAATAAAA
35127666 ATATAAAAATA
1 AT-TAAAAATA
35127677 TAGAAATTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
16 16 0.31
17 12 0.24
18 12 0.24
19 11 0.22
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.28
Consensus pattern (16 bp):
ATTAAAAATAATAAAA
Found at i:35127671 original size:8 final size:8
Alignment explanation
Indices: 35127618--35127683 Score: 53
Period size: 8 Copynumber: 7.9 Consensus size: 8
35127608 AAAAAAACAT
35127618 TAAAAATAA
1 TAAAAAT-A
35127627 TAAAAAT-
1 TAAAAATA
*
35127634 TGAAAATTA
1 T-AAAAATA
*
35127643 TTAAAATTA
1 -TAAAAATA
*
35127652 TTAAAATAA
1 TAAAAAT-A
35127661 TAAAAATA
1 TAAAAATA
35127669 TAAAAATA
1 TAAAAATA
*
35127677 TAGAAAT
1 TAAAAAT
35127684 TCTTAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
7 1 0.02
8 25 0.52
9 21 0.44
10 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (8 bp):
TAAAAATA
Found at i:35127684 original size:34 final size:34
Alignment explanation
Indices: 35127620--35127709 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 34
35127610 AAAAACATTA
*
35127620 AAAATAATAAAAAT-TGAAAATTATTAAAATTATT
1 AAAATAATAAAAATAT-AAAAATATTAAAATTATT
*
35127654 AAAATAATAAAAATATAAAAATA-TAGAAATTCTT
1 AAAATAATAAAAATATAAAAATATTA-AAATTATT
* **
35127688 AAATTTTTATAAAATATAAAAA
1 AAAATAATA-AAAATATAAAAA
35127710 ATTGCAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
33 2 0.04
34 33 0.69
35 13 0.27
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (34 bp):
AAAATAATAAAAATATAAAAATATTAAAATTATT
Found at i:35128040 original size:174 final size:170
Alignment explanation
Indices: 35127753--35128099 Score: 622
Period size: 174 Copynumber: 2.0 Consensus size: 170
35127743 AATATTATTG
*
35127753 CAAATTATTCAAAAAATAATATTAAATTCAAAAAATATAAAAAAAATCTACAATTTTATATACAC
1 CAAATTATTCAAAAAATAATATTAAATTCAAAAAATAAAAAAAAAATCTACAATTTTATATACAC
*
35127818 AGTCTCGATTGTCACTTACCTTCTCTATTTATTTCCTCACCTTAGTTTACATCTCAAAACACTCT
66 AGTCTCGATTGTCACTTACCTTCTCTATTTATTTCCTCACCTTAGTTTACATCTCAAAACACTCC
35127883 ACTATCACCAAGCTTTAGAGAGATCCGTAGTGGACAAGTTA
131 ACTATCACCAAGCTTTAGAGAGATCCGTAGTGGACAAG-TA
*
35127924 CAAATTATTCAAATAATAATATTAAATTACAAAAATATAAAAAAGAAAATCTACAATTTTATATA
1 CAAATTATTCAAAAAATAATATTAAATT-CAAAAA-ATAAAAAA-AAAATCTACAATTTTATATA
35127989 CACAGTCTCGATTGTCACTTACCTTCTCTATTTATTTCCTCACCTTAGTTTACATCTCAAAACAC
63 CACAGTCTCGATTGTCACTTACCTTCTCTATTTATTTCCTCACCTTAGTTTACATCTCAAAACAC
*
35128054 TCCACTATCACCAAGCTTTAGAGAGATTCGTAGTGGACAAGTA
128 TCCACTATCACCAAGCTTTAGAGAGATCCGTAGTGGACAAGTA
35128097 CAA
1 CAA
35128100 CAAATTGCCC
Statistics
Matches: 169, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
171 27 0.16
172 6 0.04
173 12 0.07
174 124 0.73
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (170 bp):
CAAATTATTCAAAAAATAATATTAAATTCAAAAAATAAAAAAAAAATCTACAATTTTATATACAC
AGTCTCGATTGTCACTTACCTTCTCTATTTATTTCCTCACCTTAGTTTACATCTCAAAACACTCC
ACTATCACCAAGCTTTAGAGAGATCCGTAGTGGACAAGTA
Found at i:35128421 original size:28 final size:28
Alignment explanation
Indices: 35128384--35128470 Score: 106
Period size: 27 Copynumber: 3.1 Consensus size: 28
35128374 TTATTGATTT
* *
35128384 TTTTAAATATTTTTAATAAATTTCTA-TA
1 TTTTAAATATTTTTCATAAATTT-TACAA
*
35128412 TTTTAAATATTTTTCATAACTTTTACAA
1 TTTTAAATATTTTTCATAAATTTTACAA
* *
35128440 TTTT-AATATTTTTCATAAATTATATAA
1 TTTTAAATATTTTTCATAAATTTTACAA
35128467 TTTT
1 TTTT
35128471 TATTTTGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
27 26 0.50
28 26 0.50
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTAAATATTTTTCATAAATTTTACAA
Found at i:35128468 original size:27 final size:27
Alignment explanation
Indices: 35128384--35128470 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 27
35128374 TTATTGATTT
* *
35128384 TTTTAAATATTTTTAATAAATTTCTATA
1 TTTTAAATATTTTTCATAAATTTATA-A
* *
35128412 TTTTAAATATTTTTCATAACTTTTACAA
1 TTTTAAATATTTTTCATAA-ATTTATAA
35128440 TTTT-AATATTTTTCATAAATTATATAA
1 TTTTAAATATTTTTCATAAATT-TATAA
35128467 TTTT
1 TTTT
35128471 TATTTTGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.04
27 22 0.43
28 23 0.45
29 4 0.08
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTAAATATTTTTCATAAATTTATAA
Found at i:35128512 original size:19 final size:20
Alignment explanation
Indices: 35128476--35128517 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
35128466 ATTTTTATTT
*
35128476 TGTTTTTTTAATAATTTTTAA
1 TGTTTTTGTAAT-ATTTTTAA
35128497 TGTTTTTGTAAT-TTTTTAA
1 TGTTTTTGTAATATTTTTAA
35128516 TG
1 TG
35128518 AATTATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (20 bp):
TGTTTTTGTAATATTTTTAA
Found at i:35128538 original size:9 final size:9
Alignment explanation
Indices: 35128335--35128597 Score: 68
Period size: 9 Copynumber: 28.9 Consensus size: 9
35128325 TTTTAATTTG
*
35128335 TTTTATCAT
1 TTTTATAAT
**
35128344 TTTTATGCT
1 TTTTATAAT
35128353 TTTTATAAT
1 TTTTATAAT
*
35128362 ATTTTATAAA
1 -TTTTATAAT
*
35128372 TTTTATTGATTT
1 TTTTA-T-A-AT
*
35128384 TTTTAAATAT
1 TTTTATA-AT
35128394 TTTTAATAAAT
1 TTTT-AT-AAT
*
35128405 TTCTAT-A-
1 TTTTATAAT
*
35128412 TTTTAAATAT
1 TTTTATA-AT
*
35128422 TTTTCATAAC
1 TTTT-ATAAT
*
35128432 TTTTACAAT
1 TTTTATAAT
*
35128441 TTTAAT-AT
1 TTTTATAAT
*
35128449 TTTTCATAAA
1 TTTT-ATAAT
*
35128459 TTATATAAT
1 TTTTATAAT
35128468 TTTTAT--T
1 TTTTATAAT
35128475 TTGTT-T--T
1 TT-TTATAAT
*
35128482 TTTAATAAT
1 TTTTATAAT
*
35128491 TTTTA-ATGT
1 TTTTATA-AT
*
35128500 TTTTGTAAT
1 TTTTATAAT
35128509 TTTT-TAAT
1 TTTTATAAT
** *
35128517 GAATTATATT
1 -TTTTATAAT
35128527 TTTTATAAT
1 TTTTATAAT
*
35128536 TTTT-TCAT
1 TTTTATAAT
*
35128544 TTATAATAA-
1 TT-TTATAAT
35128553 TTTTATATAT
1 TTTTATA-AT
**
35128563 TTTCCT-TTTT
1 TTT--TATAAT
35128573 TTTTATAA-
1 TTTTATAAT
35128581 TTTTATAAT
1 TTTTATAAT
35128590 TTTTATAA
1 TTTTATAA
35128598 ATTTAATCAT
Statistics
Matches: 183, Mismatches: 43, Indels: 56
0.65 0.15 0.20
Matches are distributed among these distances:
6 1 0.01
7 12 0.07
8 31 0.17
9 78 0.43
10 44 0.24
11 10 0.05
12 7 0.04
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:35128592 original size:18 final size:18
Alignment explanation
Indices: 35128479--35128602 Score: 51
Period size: 19 Copynumber: 6.8 Consensus size: 18
35128469 TTTATTTTGT
35128479 TTTTTTAATAATTTT-TAA
1 TTTTTT-ATAATTTTATAA
* *
35128497 TGTTTTTGTAATTTTTTAA
1 T-TTTTTATAATTTTATAA
*** *
35128516 TGAATTATATTTTTTATAA
1 TTTTTTATA-ATTTTATAA
*
35128535 -TTTTT-TCA-TTTATAA
1 TTTTTTATAATTTTATAA
* * **
35128550 TAATTTTATATATTTTCCTTT
1 T-TTTTTATA-ATTTT-ATAA
35128571 TTTTTTATAATTTTATAA
1 TTTTTTATAATTTTATAA
*
35128589 -TTTTTATAAATTTA
1 TTTTTTATAATTTTA
35128603 ATCATAAAAT
Statistics
Matches: 75, Mismatches: 22, Indels: 19
0.65 0.19 0.16
Matches are distributed among these distances:
15 7 0.09
17 18 0.24
18 16 0.21
19 22 0.29
20 10 0.13
21 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTTATAATTTTATAA
Found at i:35129052 original size:49 final size:49
Alignment explanation
Indices: 35128999--35129094 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
35128989 AGTTGTAGAA
35128999 TTCATTGTGATGATGGATTATAAATTTAAGGATTTTAATATATATTGAG
1 TTCATTGTGATGATGGATTATAAATTTAAGGATTTTAATATATATTGAG
35129048 TTCATTGTGATGATGGATTATAAATTTAAGGATTTTAATATATATTG
1 TTCATTGTGATGATGGATTATAAATTTAAGGATTTTAATATATATTG
35129095 TAATCGTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (49 bp):
TTCATTGTGATGATGGATTATAAATTTAAGGATTTTAATATATATTGAG
Found at i:35134772 original size:20 final size:20
Alignment explanation
Indices: 35134747--35134786 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
35134737 TCCACCTCAT
35134747 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
*
35134767 GCATCGCATTATATGCATTA
1 GCATCGCATCATATGCATTA
35134787 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (20 bp):
GCATCGCATCATATGCATTA
Found at i:35142933 original size:45 final size:45
Alignment explanation
Indices: 35142875--35143399 Score: 404
Period size: 44 Copynumber: 11.8 Consensus size: 45
35142865 GATCGAATAT
* * * *
35142875 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAAATCGAAGAAA
1 ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
*** *
35142920 ACAGATCTTGTCTTCATGTACTGGT-GTGAAGTAGATCAAAGATA
1 ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
* * ** * *
35142964 CCAGATCTTGCCTTCCCATACTGGTGACGAAGCAGATCGAAGAAA
1 ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
*** * *
35143009 ACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATA
1 ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
* * * *
35143053 CCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAA
1 ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
* *** * *
35143098 ACATATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAG-AT
1 ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
* * * * *
35143141 ACTAGATCTTGCCTTCCCATATTGGTGGCGAAGCAGATCGAAGAAA
1 AC-AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
* *** *
35143187 ACAGATATTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAG-AA
1 ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
* *
35143230 ACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAA-AAA
1 ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-AAAGAAA
* * *** * *
35143275 ATAGATCTTATCTTCATGTACTGG-CGTGAAGTAGATCAAAGATA
1 ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
* * * * * * ** * *
35143319 GCAGGTCCTGTCTTCCTATA-TCGGTAGTGAAGTGGATTGAA-TAT
1 ACAGATCTTGTCTTCCCATACT-GGTGGTGAAGTAGATCAAAGAAA
* * *
35143363 ACAGATTTTATCTTCCCATACTGGTGGCGAAGTAGAT
1 ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGAT
35143400 TGAAGATTAC
Statistics
Matches: 360, Mismatches: 108, Indels: 25
0.73 0.22 0.05
Matches are distributed among these distances:
43 28 0.08
44 175 0.49
45 154 0.43
46 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (45 bp):
ACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
Found at i:35142995 original size:89 final size:89
Alignment explanation
Indices: 35142859--35143318 Score: 717
Period size: 89 Copynumber: 5.2 Consensus size: 89
35142849 TATTGGTAGC
* * * * *
35142859 GAAGTGGATCGAATATA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAAATCGAAGAAAACA
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACA
*
35142923 GATCTTGTCTTCATGTACTGGTGT
66 GATCTTGTCTTCATGTACTGGCGT
*
35142947 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGACGAAGCAGATCGAAGAAAACA
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACA
35143012 GATCTTGTCTTCATGTACTGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
*
35143036 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAACA
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACA
*
35143101 TATCTTGTCTTCATGTACTGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
* *
35143125 GAAGTAGATCAAAGATACTAGATCTTGCCTTCCCATATTGGTGGCGAAGCAGATCGAAGAAAACA
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACA
*
35143190 GATATTGTCTTCATGTACTGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
* * * * * * * *
35143214 GAAGTAGATCAAAGA-AACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAAAAAATA
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACA
*
35143278 GATCTTATCTTCATGTACTGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
35143302 GAAGTAGATCAAAGATA
1 GAAGTAGATCAAAGATA
35143319 GCAGGTCCTG
Statistics
Matches: 343, Mismatches: 27, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
88 90 0.26
89 253 0.74
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (89 bp):
GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACA
GATCTTGTCTTCATGTACTGGCGT
Found at i:35143386 original size:88 final size:87
Alignment explanation
Indices: 35142859--35143377 Score: 524
Period size: 89 Copynumber: 5.9 Consensus size: 87
35142849 TATTGGTAGC
* * * * * *
35142859 GAAGTGGATCGAATATACAGATCTTGTCTTCCCATA-CTGGTGGCGAAGCAAATCGAAGAAAACA
1 GAAGTAGATCAAAGATACAGATCTTGTCTTCCCATATC-GGTGGTGAAGTAGATCGAA-AAAACA
* * *
35142923 GATCTTGTCTTCATGTACTGGTGT
64 GATATTATCTTCATGTACTGGCGT
* ** *
35142947 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATA-CTGGTGACGAAGCAGATCGAAGAAAAC
1 GAAGTAGATCAAAGATA-CAGATCTTGTCTTCCCATATC-GGTGGTGAAGTAGATCGAA-AAAAC
* *
35143011 AGATCTTGTCTTCATGTACTGGCGT
63 AGATATTATCTTCATGTACTGGCGT
* * * *
35143036 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATA-CTGGTGGCGAAGCAGATCAAAGAAAAC
1 GAAGTAGATCAAAGATA-CAGATCTTGTCTTCCCATATC-GGTGGTGAAGTAGATCGAA-AAAAC
* * *
35143100 ATATCTTGTCTTCATGTACTGGCGT
63 AGATATTATCTTCATGTACTGGCGT
* * * *
35143125 GAAGTAGATCAAAGATACTAGATCTTGCCTTCCCATATTGGTGGCGAAGCAGATCGAAGAAAACA
1 GAAGTAGATCAAAGATAC-AGATCTTGTCTTCCCATATCGGTGGTGAAGTAGATCGAA-AAAACA
*
35143190 GATATTGTCTTCATGTACTGGCGT
64 GATATTATCTTCATGTACTGGCGT
* * * *
35143214 GAAGTAGATCAAAGAAACAGATCTTGTCTCCCCATA-CTGGTGGTGGAGTAGATCGAAAAAAATA
1 GAAGTAGATCAAAGATACAGATCTTGTCTTCCCATATC-GGTGGTGAAGTAGATCG-AAAAAACA
*
35143278 GATCTTATCTTCATGTACTGGCGT
64 GATATTATCTTCATGTACTGGCGT
* * * * * * * *
35143302 GAAGTAGATCAAAGATAGCAGGTCCTGTCTTCCTATATCGGTAGTGAAGTGGATTGAATATACAG
1 GAAGTAGATCAAAGATA-CAGATCTTGTCTTCCCATATCGGTGGTGAAGTAGATCGAAAAAACAG
*
35143367 ATTTTATCTTC
65 ATATTATCTTC
35143378 CCATACTGGT
Statistics
Matches: 387, Mismatches: 37, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
88 104 0.27
89 282 0.73
90 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (87 bp):
GAAGTAGATCAAAGATACAGATCTTGTCTTCCCATATCGGTGGTGAAGTAGATCGAAAAAACAGA
TATTATCTTCATGTACTGGCGT
Found at i:35145345 original size:15 final size:15
Alignment explanation
Indices: 35145322--35145351 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35145312 AAGTTTTCAA
35145322 ATACGTACATACTTT
1 ATACGTACATACTTT
*
35145337 ATACTTACATACTTT
1 ATACGTACATACTTT
35145352 TTTATATTAT
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:0.33, C:0.20, G:0.03, T:0.43
Consensus pattern (15 bp):
ATACGTACATACTTT
Found at i:35148287 original size:18 final size:18
Alignment explanation
Indices: 35148243--35148287 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
35148233 ACCAATACGA
35148243 TATAAATAAATTAAAATT
1 TATAAATAAATTAAAATT
* *
35148261 TATATATAAATTATTAATT
1 TATAAATAAATTA-AAATT
35148280 TA-AAATAA
1 TATAAATAA
35148288 TTGAAATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAAATAAATTAAAATT
Found at i:35157675 original size:20 final size:20
Alignment explanation
Indices: 35157650--35157700 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
35157640 TTGTATGGGA
*
35157650 TTTGCACTTGGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
35157670 TTTGCACTTCGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* *
35157690 TATACACTTCG
1 TTTGCACTTCG
35157701 ATGTCTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.31, G:0.24, T:0.35
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:35157879 original size:7 final size:7
Alignment explanation
Indices: 35157867--35157895 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
35157857 AAGATATTAG
35157867 TAAATGT
1 TAAATGT
35157874 TAAATGT
1 TAAATGT
35157881 TAAATGT
1 TAAATGT
35157888 TAAATGT
1 TAAATGT
35157895 T
1 T
35157896 CGATGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (7 bp):
TAAATGT
Found at i:35158175 original size:15 final size:15
Alignment explanation
Indices: 35158155--35158191 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
35158145 AGTTTGAGAC
35158155 GAATGATGAACTACA
1 GAATGATGAACTACA
*
35158170 GAATGATGAATTACA
1 GAATGATGAACTACA
*
35158185 TAATGAT
1 GAATGAT
35158192 TATTAGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (15 bp):
GAATGATGAACTACA
Found at i:35159854 original size:34 final size:35
Alignment explanation
Indices: 35159786--35159858 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
35159776 AATGATGTTA
* **
35159786 AATTGTATGTATTTATTTTGTACATAGCCGAATTG
1 AATTGTATGTATGTATAATGTACATAGCCGAATTG
* *
35159821 AATTGTATGTATGTATAAT-TACATTGCCTAATTG
1 AATTGTATGTATGTATAATGTACATAGCCGAATTG
35159855 AATT
1 AATT
35159859 TAGCATGGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (35 bp):
AATTGTATGTATGTATAATGTACATAGCCGAATTG
Found at i:35163872 original size:13 final size:13
Alignment explanation
Indices: 35163856--35163885 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35163846 ATTAATTTAG
35163856 TTAATTTAATTAA
1 TTAATTTAATTAA
*
35163869 TTAATTTAATTGA
1 TTAATTTAATTAA
35163882 TTAA
1 TTAA
35163886 ATAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:35170621 original size:13 final size:13
Alignment explanation
Indices: 35170603--35170631 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
35170593 ATGAATAAAT
35170603 AGGGTTTGTATGA
1 AGGGTTTGTATGA
35170616 AGGGTTTGTATGA
1 AGGGTTTGTATGA
35170629 AGG
1 AGG
35170632 TTCATCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.34
Consensus pattern (13 bp):
AGGGTTTGTATGA
Found at i:35170674 original size:81 final size:81
Alignment explanation
Indices: 35170539--35170690 Score: 259
Period size: 81 Copynumber: 1.9 Consensus size: 81
35170529 TGGCTCGGGT
* * * *
35170539 TTTGTATAAAGGTTCATCAAGAAGTGTATTCTGACTCAAATATAGGTACTAAAGATGAATAAATA
1 TTTGTATAAAGGTTCATCAAGAAGTATATTCTAACTCAAATATAAGTAATAAAGATGAATAAATA
35170604 GGGTTTGTATGAAGGG
66 GGGTTTGTATGAAGGG
*
35170620 TTTGTATGAAGGTTCATCAAGAAGTATATTCTAACTCAAATATAAGTAATAAAGATGAATAAATA
1 TTTGTATAAAGGTTCATCAAGAAGTATATTCTAACTCAAATATAAGTAATAAAGATGAATAAATA
35170685 GGGTTT
66 GGGTTT
35170691 TTTTTTACTC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.33
Consensus pattern (81 bp):
TTTGTATAAAGGTTCATCAAGAAGTATATTCTAACTCAAATATAAGTAATAAAGATGAATAAATA
GGGTTTGTATGAAGGG
Found at i:35172852 original size:7 final size:7
Alignment explanation
Indices: 35172840--35172874 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
35172830 ACTATGACAA
35172840 GAAATAT
1 GAAATAT
35172847 GAAATAT
1 GAAATAT
35172854 GAAATAT
1 GAAATAT
35172861 GAAATAT
1 GAAATAT
35172868 GAAATAT
1 GAAATAT
35172875 AATATTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (7 bp):
GAAATAT
Found at i:35176157 original size:17 final size:17
Alignment explanation
Indices: 35176132--35176165 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35176122 TAAGAAAAAA
*
35176132 TTGAGAAAAATCAATTC
1 TTGAAAAAAATCAATTC
*
35176149 TTGAAAAAAATTAATTC
1 TTGAAAAAAATCAATTC
35176166 AGCCCCTACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (17 bp):
TTGAAAAAAATCAATTC
Found at i:35176361 original size:10 final size:9
Alignment explanation
Indices: 35176348--35176397 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
35176338 TAAATAATTA
35176348 TAAAAATCAT
1 TAAAAAT-AT
35176358 TAAAAATA-
1 TAAAAATAT
35176366 TAAAAATTAT
1 TAAAAA-TAT
35176376 T--AAATAT
1 TAAAAATAT
35176383 TATAAAATAT
1 TA-AAAATAT
35176393 TAAAA
1 TAAAA
35176398 TTTTATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
7 4 0.11
8 9 0.26
9 6 0.17
10 16 0.46
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAAATAT
Found at i:35176369 original size:18 final size:17
Alignment explanation
Indices: 35176346--35176397 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
35176336 CATAAATAAT
35176346 TATAAAAATCATTAAAAA
1 TATAAAAAT-ATTAAAAA
*
35176364 TATAAAAATTATTAAATA
1 TATAAAAA-TATTAAAAA
35176382 T-TATAAAATATTAAAA
1 TATA-AAAATATTAAAA
35176398 TTTTATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 9 0.30
18 20 0.67
19 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TATAAAAATATTAAAAA
Found at i:35176389 original size:26 final size:27
Alignment explanation
Indices: 35176337--35176399 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 27
35176327 TGTTTTTCTC
35176337 ATAAATAATTATAAAAATCATTAAAAAT
1 ATAAA-AATTATAAAAATCATTAAAAAT
*
35176365 ATAAAAATTAT-TAAAT-ATTATAAAAT
1 ATAAAAATTATAAAAATCATTA-AAAAT
*
35176391 ATTAAAATT
1 ATAAAAATT
35176400 TTATATAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 4 0.12
26 17 0.53
27 6 0.19
28 5 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
ATAAAAATTATAAAAATCATTAAAAAT
Found at i:35176398 original size:18 final size:18
Alignment explanation
Indices: 35176339--35176431 Score: 59
Period size: 18 Copynumber: 5.0 Consensus size: 18
35176329 TTTTTCTCAT
35176339 AAATAATTATAAAAATCATTA
1 AAAT-ATTAT-AAAAT-ATTA
35176360 AAA-A-TATAAAA-ATTA
1 AAATATTATAAAATATTA
35176375 TTAAATATTATAAAATATTA
1 --AAATATTATAAAATATTA
* *
35176395 AAATTTTATATAAA-GTTA
1 AAATATTATA-AAATATTA
* *
35176413 AACATGTTGTAAAATATTA
1 AA-ATATTATAAAATATTA
35176432 TGGAACATAC
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
15 4 0.07
17 7 0.12
18 21 0.36
19 20 0.34
20 4 0.07
21 3 0.05
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATATTATAAAATATTA
Found at i:35179097 original size:15 final size:16
Alignment explanation
Indices: 35179049--35179097 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
35179039 TCTTATATAA
35179049 TGAAACTCTAGAAT-G
1 TGAAACTCTAGAATAG
*
35179064 TGAAACTCTAGATTA-
1 TGAAACTCTAGAATAG
*
35179079 TGAAACTATA-AATAG
1 TGAAACTCTAGAATAG
35179094 TGAA
1 TGAA
35179098 GCTGCAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 3 0.10
15 26 0.90
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (16 bp):
TGAAACTCTAGAATAG
Found at i:35180726 original size:16 final size:16
Alignment explanation
Indices: 35180705--35180738 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
35180695 TAATTTTTCC
35180705 TTAATTTTTGGTCAAT
1 TTAATTTTTGGTCAAT
35180721 TTAATTTTTGGTCAAT
1 TTAATTTTTGGTCAAT
35180737 TT
1 TT
35180739 GAGTGCCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (16 bp):
TTAATTTTTGGTCAAT
Found at i:35203454 original size:23 final size:23
Alignment explanation
Indices: 35203428--35203475 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
35203418 TTGATATTAC
35203428 ATCTTATCACATCGATATATCCT
1 ATCTTATCACATCGATATATCCT
35203451 ATCTTATCACATCGATATATCCT
1 ATCTTATCACATCGATATATCCT
35203474 AT
1 AT
35203476 ATGGCATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (23 bp):
ATCTTATCACATCGATATATCCT
Found at i:35214074 original size:50 final size:50
Alignment explanation
Indices: 35213997--35214185 Score: 207
Period size: 50 Copynumber: 3.8 Consensus size: 50
35213987 TCTTGTACTA
* * ** * *
35213997 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTTATATTGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTG
* * * ** * *
35214047 CCCATGCCATGTCCTAGACATAGTCTTACGGGGGACCTCTCATCTCGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTG
* *
35214097 CCAATGCCATGTCCCAGACATGTTATTACATGGGACCTCTTATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTG
** * *
35214147 CCAACACCATGTCCGAGACATGGTCTTACATGAGACCTC
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC
35214186 ATTCCGTTAA
Statistics
Matches: 111, Mismatches: 28, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 111 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTG
Found at i:35214184 original size:100 final size:100
Alignment explanation
Indices: 35213997--35214185 Score: 234
Period size: 100 Copynumber: 1.9 Consensus size: 100
35213987 TCTTGTACTA
* * ** * * ** *
35213997 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTTATATTGGTGCCCATGCCATGTCCT
1 CCAATGCCATATCCCAGACATGGTATTACATGGGACCTCTTATATCGGTGCCAACACCATGTCCG
* *
35214062 AGACATAGTCTTACGGGGGACCTCTCATCTCGATG
66 AGACATAGTCTTACAGGAGACCTCTCATCTCGATG
* * *
35214097 CCAATGCCATGTCCCAGACATGTTATTACATGGGACCTCTTATCTCGGTGCCAACACCATGTCCG
1 CCAATGCCATATCCCAGACATGGTATTACATGGGACCTCTTATATCGGTGCCAACACCATGTCCG
* *
35214162 AGACATGGTCTTACATGAGACCTC
66 AGACATAGTCTTACAGGAGACCTC
35214186 ATTCCGTTAA
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
100 73 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (100 bp):
CCAATGCCATATCCCAGACATGGTATTACATGGGACCTCTTATATCGGTGCCAACACCATGTCCG
AGACATAGTCTTACAGGAGACCTCTCATCTCGATG
Found at i:35215080 original size:17 final size:19
Alignment explanation
Indices: 35215058--35215094 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
35215048 CTAAATGACT
35215058 AAAATA-CC-TTTCACTTA
1 AAAATATCCATTTCACTTA
35215075 AAAATATCCTATTTCACTTA
1 AAAATATCC-ATTTCACTTA
35215095 TCTCATGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
20 9 0.53
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATCCATTTCACTTA
Found at i:35220211 original size:23 final size:23
Alignment explanation
Indices: 35220181--35220229 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
35220171 TTTTACTTAA
35220181 TTATAATGCTTGTGTAACACCCC
1 TTATAATGCTTGTGTAACACCCC
*
35220204 TTATAATGCTTGTGTGACACCCC
1 TTATAATGCTTGTGTAACACCCC
35220227 TTA
1 TTA
35220230 CTCGTATTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (23 bp):
TTATAATGCTTGTGTAACACCCC
Found at i:35225884 original size:23 final size:21
Alignment explanation
Indices: 35225845--35225915 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 21
35225835 ATCTTTAAAT
35225845 ATATGTAATCTT--AGATATG
1 ATATGTAATCTTAGAGATATG
*
35225864 ATATGTAATCTTTAGAAGATACG
1 ATATGTAATC-TTAG-AGATATG
* *
35225887 ATTCTGTAATCTTAGAGATTTG
1 A-TATGTAATCTTAGAGATATG
*
35225909 ATTTGTA
1 ATATGTA
35225916 GATAGCTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.24
20 2 0.05
21 5 0.12
22 6 0.14
23 11 0.26
24 8 0.19
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (21 bp):
ATATGTAATCTTAGAGATATG
Found at i:35227827 original size:85 final size:85
Alignment explanation
Indices: 35227717--35227883 Score: 221
Period size: 85 Copynumber: 2.0 Consensus size: 85
35227707 AGGTTTTTGA
* * * * * * *
35227717 TGGTGTCCGAGGCTTCCGTATGTCCAAGCA-CATAGGT-TCTGATGTTGCCCGATGCTCCCACGC
1 TGGTGTCCGAGACTCCCGCACGTCCAAGCACCA-AGGTGTC-GATGCTACCCGATGCTCCCACAC
*
35227780 AACCAAGGGCCTATGTTGTTGC
64 AACCAAAGGCCTATGTTGTTGC
*
35227802 TGGTGTCCGAGACTCCCGCACGTCCAAGCACCAAGGTGTCGATGCTACCCGATGCTCCCGCACAA
1 TGGTGTCCGAGACTCCCGCACGTCCAAGCACCAAGGTGTCGATGCTACCCGATGCTCCCACACAA
35227867 CCAAAGGCCTATGTTGT
66 CCAAAGGCCTATGTTGT
35227884 CAATGATATA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
85 67 0.94
86 4 0.06
ACGTcount: A:0.20, C:0.31, G:0.26, T:0.23
Consensus pattern (85 bp):
TGGTGTCCGAGACTCCCGCACGTCCAAGCACCAAGGTGTCGATGCTACCCGATGCTCCCACACAA
CCAAAGGCCTATGTTGTTGC
Found at i:35229705 original size:27 final size:26
Alignment explanation
Indices: 35229675--35229725 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
35229665 ATGAAATTCT
*
35229675 TACAAA-CAACATGATTGATTAACAATA
1 TACAAAGCAA-ATGA-TGAATAACAATA
35229702 TACAAAGCAAATGATGAATAACAA
1 TACAAAGCAAATGATGAATAACAA
35229726 ATTAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 10 0.45
28 3 0.14
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.22
Consensus pattern (26 bp):
TACAAAGCAAATGATGAATAACAATA
Found at i:35230017 original size:23 final size:23
Alignment explanation
Indices: 35229973--35230017 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
35229963 ATAATAAGTT
**
35229973 TAAAAATAATATTAAGCCAATAA
1 TAAAAATAATATTAAAACAATAA
* *
35229996 TAAAAATAATGTTAAAATAATA
1 TAAAAATAATATTAAAACAATA
35230018 TATGAACATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAAAATAATATTAAAACAATAA
Found at i:35231919 original size:85 final size:85
Alignment explanation
Indices: 35231762--35231932 Score: 209
Period size: 85 Copynumber: 2.0 Consensus size: 85
35231752 TCCAGTTGGC
* * * ** *
35231762 AAGACTTGATGCAATCTGCTCTACTGCAACTTCAGAAAGATAAGATCGGTCTCTTCTGTCTATTC
1 AAGACCTGATGCAATCTACTCTACTGCAACTTCAGAAAGATAAGATCGGTATCTTCAATCTACTC
35231827 CAATGTAATCTCAGGGAGAT
66 CAATGTAATCTCAGGGAGAT
* * * ** *
35231847 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTT-AATCTGCT
1 AAGACCTGATGCAATCTACTCTACTGCAACTTCAGAAAGATAAGAT-CGGTATCTTCAATCTACT
*
35231911 CCACTGTAATCTCAGGGAGAT
65 CCAATGTAATCTCAGGGAGAT
35231932 A
1 A
35231933 GGATTACTAG
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 66 0.92
86 6 0.08
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (85 bp):
AAGACCTGATGCAATCTACTCTACTGCAACTTCAGAAAGATAAGATCGGTATCTTCAATCTACTC
CAATGTAATCTCAGGGAGAT
Found at i:35231931 original size:44 final size:45
Alignment explanation
Indices: 35231825--35232499 Score: 208
Period size: 44 Copynumber: 14.5 Consensus size: 45
35231815 TTCTGTCTAT
* * * * *
35231825 TCCAATGTAATCTCAGGGAGATAAGA-CC-TGA--TGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATCTTCAATCTGC
* *
35231866 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATCTT-AATCTGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATCTTCAATCTGC
* * *
35231910 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTATCTTCAATCTGC
* * * * *
35231954 TCCACTATAATCTCAGGGAAATAAGATTTCTGGTTTCAATCTGATGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGA--TC--CTTT--ATCT--T-CAATCTGC
* * *
35232008 TCTACTGTAA-CTTCAGAGAGATAAGA-CCTTTAT-TTCAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATCTTCAATCTGC
* * * *
35232051 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAACCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTATCTTCAATCTGC
* * * * *
35232095 TCCGCTGTAATCTCAGAGAGATAAGATTTCTGGTTTCAATCTGATACGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGA--TC--CTTT--ATCT--T-CAATCTGC
* * * * * * *
35232149 TCTATTGTAA-CTTTAGAGAGATAAGATCCTATAT-TTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATCTTCAATCTGC
* * * ** * *
35232193 TGCACTGTAATCTCAGGGAGATAGGAT--TACTAGATTCGATCTGT
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTATCTTCAATCTGC
* * * *
35232237 TCCGCTGTAATCTCAGGGAGATAAGATTTCTGGTATCAATCTGATGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGA-TCCT--T-T--ATCT--T-CAATCTGC
* * * *
35232291 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTTAT-TTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATCTTCAATCTGC
* * * * *
35232335 TCCACTGTAATCTCAGGGATATAGGAT--TACTAGCTTCGATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTATCTTCAATCTGC
** * * *
35232379 TCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGA--TC---CTT-TATCT--T-CAATCTGC
* * * *
35232433 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTTAT-TTTAATCTAC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATCTTCAATCTGC
*
35232477 TCCACTGTAATCTCAGAGAGATA
1 TCCACTGTAATCTCAGGGAGATA
35232500 GGATTACTAG
Statistics
Matches: 464, Mismatches: 104, Indels: 129
0.67 0.15 0.19
Matches are distributed among these distances:
40 1 0.00
41 21 0.05
42 6 0.01
43 39 0.08
44 222 0.48
45 9 0.02
46 4 0.01
47 6 0.01
48 6 0.01
49 9 0.02
50 5 0.01
51 14 0.03
52 4 0.01
53 11 0.02
54 107 0.23
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (45 bp):
TCCACTGTAATCTCAGGGAGATAAGATCCTTTATCTTCAATCTGC
Found at i:35232251 original size:142 final size:142
Alignment explanation
Indices: 35231852--35232518 Score: 1111
Period size: 142 Copynumber: 4.7 Consensus size: 142
35231842 GAGATAAGAC
* *
35231852 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTTAATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
35231917 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTATAATCTCAGGGAAATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
35231982 TCTGGTTTCAAT
131 TCTGGTTTCAAT
*
35231994 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGA-CCTTTATTTCAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
35232058 TAATCTCAGGGAGATAGGATTACTAGCTTCAACCTGCTCCGCTGTAATCTCAGAGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
35232123 TCTGGTTTCAAT
131 TCTGGTTTCAAT
* * * * *
35232135 CTGATACGATCTACTCTATTGTAACTTTAGAGAGATAAGATCCTATATTTTAATCCGCTGCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
35232200 TAATCTCAGGGAGATAGGATTACTAGATTCGATCTGTTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
*
35232265 TCTGGTATCAAT
131 TCTGGTTTCAAT
35232277 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
35232342 TAATCTCAGGGATATAGGATTACTAGCTTCGATCTGCTCTGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
*
35232407 TCTGGCTTCAAT
131 TCTGGTTTCAAT
**
35232419 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTACTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
*
35232484 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
35232519 ACTTCCTTAC
Statistics
Matches: 488, Mismatches: 36, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
141 130 0.27
142 358 0.73
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGTTTCAAT
Found at i:35244636 original size:27 final size:26
Alignment explanation
Indices: 35244606--35244656 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
35244596 ATGAAATTCT
*
35244606 TACAAA-CAACATGATTGATTAACAATA
1 TACAAAGCAA-ATGA-TGAATAACAATA
35244633 TACAAAGCAAATGATGAATAACAA
1 TACAAAGCAAATGATGAATAACAA
35244657 ATTAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 10 0.45
28 3 0.14
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.22
Consensus pattern (26 bp):
TACAAAGCAAATGATGAATAACAATA
Found at i:35244948 original size:23 final size:23
Alignment explanation
Indices: 35244904--35244948 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
35244894 ATAATAAGTT
**
35244904 TAAAAATAATATTAAGCCAATAA
1 TAAAAATAATATTAAAACAATAA
* *
35244927 TAAAAATAATGTTAAAATAATA
1 TAAAAATAATATTAAAACAATA
35244949 TATGAACATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAAAATAATATTAAAACAATAA
Found at i:35250408 original size:17 final size:17
Alignment explanation
Indices: 35250386--35250418 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35250376 AAACAACATA
35250386 ACTCTTGACCTTTCATG
1 ACTCTTGACCTTTCATG
35250403 ACTCTTGACCTTTCAT
1 ACTCTTGACCTTTCAT
35250419 ATAACATAAC
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:0.18, C:0.30, G:0.09, T:0.42
Consensus pattern (17 bp):
ACTCTTGACCTTTCATG
Found at i:35254735 original size:17 final size:17
Alignment explanation
Indices: 35254713--35254745 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35254703 AAACAACATA
35254713 ACTCTTGACCTTTCATG
1 ACTCTTGACCTTTCATG
35254730 ACTCTTGACCTTTCAT
1 ACTCTTGACCTTTCAT
35254746 ATAACATAAC
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:0.18, C:0.30, G:0.09, T:0.42
Consensus pattern (17 bp):
ACTCTTGACCTTTCATG
Found at i:35256798 original size:22 final size:21
Alignment explanation
Indices: 35256742--35256785 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
35256732 CCAAGAATAG
35256742 AATGCTTCAAAATCTTGGAGA
1 AATGCTTCAAAATCTTGGAGA
35256763 AATGCTTCAAAATCTTGGAGA
1 AATGCTTCAAAATCTTGGAGA
35256784 AA
1 AA
35256786 ATTTTTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (21 bp):
AATGCTTCAAAATCTTGGAGA
Found at i:35257409 original size:22 final size:22
Alignment explanation
Indices: 35257381--35257431 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
35257371 CTCTCTAATC
35257381 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
35257403 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
35257425 CTCTCAA
1 CTCTCAA
35257432 ACCCATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Done.