Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 41 of 198
Found at i:12226989 original size:8 final size:8
Alignment explanation
Indices: 12226976--12227023 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
12226966 ATTTTCTTCG
12226976 TTTTTTCT
1 TTTTTTCT
*
12226984 TTTTTTTT
1 TTTTTTCT
12226992 TTTATTTCT
1 TTT-TTTCT
**
12227001 TTGGTTCT
1 TTTTTTCT
12227009 TTGTTTTCT
1 TT-TTTTCT
12227018 TTTTTT
1 TTTTTT
12227024 GCACCAAACG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
8 20 0.62
9 12 0.38
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.83
Consensus pattern (8 bp):
TTTTTTCT
Found at i:12227638 original size:3 final size:3
Alignment explanation
Indices: 12227620--12227748 Score: 63
Period size: 3 Copynumber: 43.3 Consensus size: 3
12227610 ATTTTTTAAT
* * * * *
12227620 TTA TTA ATA CTA TTA TTA TTA TTA CTA TTA TTA TTA TAA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
12227668 TCGTA TTA GT- TTA -TA TTT TTT TTA -CA TTA TT- TTA TT- TTA TTA
1 T--TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
12227710 TGTA TTG TTA TT- TTAA TTA TTT TTA TCA TTTA TTA TTA T
1 T-TA TTA TTA TTA TT-A TTA TTA TTA TTA -TTA TTA TTA T
12227749 CTAATTACAT
Statistics
Matches: 94, Mismatches: 21, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
2 10 0.11
3 74 0.79
4 7 0.07
5 3 0.03
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:12228944 original size:19 final size:19
Alignment explanation
Indices: 12228922--12228963 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
12228912 TAAAAAGATA
12228922 AACTTAATTTCGAAGATTG
1 AACTTAATTTCGAAGATTG
12228941 AACTTAATTTCGAAGATTG
1 AACTTAATTTCGAAGATTG
12228960 AACT
1 AACT
12228964 GTTGCACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
AACTTAATTTCGAAGATTG
Found at i:12246596 original size:16 final size:16
Alignment explanation
Indices: 12246575--12246609 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12246565 AATGGCGGAT
*
12246575 TGTTTAGTTGAAGAAA
1 TGTTTACTTGAAGAAA
12246591 TGTTTACTTGAAGAAA
1 TGTTTACTTGAAGAAA
12246607 TGT
1 TGT
12246610 CATGTTGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.40
Consensus pattern (16 bp):
TGTTTACTTGAAGAAA
Found at i:12248519 original size:29 final size:29
Alignment explanation
Indices: 12248477--12248794 Score: 273
Period size: 29 Copynumber: 10.9 Consensus size: 29
12248467 TCATCAATCA
* *
12248477 ATGAAAAGGGATAGTTTCGACTATCGATT
1 ATGAAAAGGGATGGTTTCGACCATCGATT
* * * * *
12248506 ATGAAAGGGGATAGTTTCGACTATCAAAT
1 ATGAAAAGGGATGGTTTCGACCATCGATT
* * * *
12248535 ATGAAAAGGGATGGTTACGACTATCAACT
1 ATGAAAAGGGATGGTTTCGACCATCGATT
* *
12248564 ATGAAAAGGGATGGTGAT-GAACATCG-TAT
1 ATGAAAAGGGATGGT-TTCGACCATCGAT-T
** *
12248593 ATGAAAAGGGATAATGTT-GACTATCGATT
1 ATGAAAAGGGATGGT-TTCGACCATCGATT
* * *
12248622 ATGAAAAGGGATAGTTTCGACTATCGACT
1 ATGAAAAGGGATGGTTTCGACCATCGATT
* ** * *
12248651 ATGGAAAGGGATGGTGACGACCATCAACT
1 ATGAAAAGGGATGGTTTCGACCATCGATT
** *
12248680 ATGAAAAGGGATGGTGACGACCATTGATT
1 ATGAAAAGGGATGGTTTCGACCATCGATT
** *
12248709 GATGAAAAGGGATGGTGACGACCACCGATTT
1 -ATGAAAAGGGATGGTTTCGACCATCGA-TT
** *
12248740 ATGAAAAGGGATGGTGACGACCATCGAAT
1 ATGAAAAGGGATGGTTTCGACCATCGATT
12248769 ATGAAAAGGGATGGTTTCGACCATCG
1 ATGAAAAGGGATGGTTTCGACCATCG
12248795 TTAGCGTACT
Statistics
Matches: 247, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
28 2 0.01
29 191 0.77
30 52 0.21
31 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATGGTTTCGACCATCGATT
Found at i:12248596 original size:87 final size:87
Alignment explanation
Indices: 12248477--12248794 Score: 334
Period size: 87 Copynumber: 3.6 Consensus size: 87
12248467 TCATCAATCA
* ** * * * * *
12248477 ATGAAAAGGGATAGTTTCGACTATCGATTATGAAAGGGGATAGTTTCGACTATCAAATATGAAAA
1 ATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATAGTTTCGACTATCGATTATGAAAA
12248542 GGGATGGTTACGACTATCAACT
66 GGGATGGTTACGACTATCAACT
* * * *
12248564 ATGAAAAGGGATGGTGATGAACATCGTATATGAAAAGGGATAATGTT-GACTATCGATTATGAAA
1 ATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATAGT-TTCGACTATCGATTATGAAA
* * *
12248628 AGGGATAGTTTCGACTATCGACT
65 AGGGATGGTTACGACTATCAACT
* * ** * *
12248651 ATGGAAAGGGATGGTGACGACCATC-AACTATGAAAAGGGATGGTGACGACCATTGATTGATGAA
1 ATGAAAAGGGATGGTGACGACCATCGAA-TATGAAAAGGGATAGTTTCGACTATCGATT-ATGAA
* * * **
12248715 AAGGGATGGTGACGACCACCGATTT
64 AAGGGATGGTTACGACTATC-AACT
* *
12248740 ATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATGGTTTCGACCATCG
1 ATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATAGTTTCGACTATCG
12248795 TTAGCGTACT
Statistics
Matches: 188, Mismatches: 37, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
86 1 0.01
87 114 0.61
88 22 0.12
89 49 0.26
90 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (87 bp):
ATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATAGTTTCGACTATCGATTATGAAAA
GGGATGGTTACGACTATCAACT
Found at i:12261227 original size:21 final size:20
Alignment explanation
Indices: 12261201--12261246 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
12261191 TGTATTCTTC
12261201 AGTTAAAGATTAACACATGGA
1 AGTTAAAGA-TAACACATGGA
*
12261222 AGTT-AATATAACACATGGA
1 AGTTAAAGATAACACATGGA
12261241 AGTTAA
1 AGTTAA
12261247 TATTCTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 15 0.65
20 4 0.17
21 4 0.17
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (20 bp):
AGTTAAAGATAACACATGGA
Found at i:12261235 original size:19 final size:19
Alignment explanation
Indices: 12261211--12261249 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12261201 AGTTAAAGAT
12261211 TAACACATGGAAGTTAATA
1 TAACACATGGAAGTTAATA
12261230 TAACACATGGAAGTTAATA
1 TAACACATGGAAGTTAATA
12261249 T
1 T
12261250 TCTTCTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (19 bp):
TAACACATGGAAGTTAATA
Found at i:12264043 original size:17 final size:17
Alignment explanation
Indices: 12264021--12264054 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12264011 CACTAAAATG
*
12264021 AAAATGTAATAACAAAA
1 AAAATGCAATAACAAAA
*
12264038 AAAATGCAATGACAAAA
1 AAAATGCAATAACAAAA
12264055 TGTACTTATC
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:0.68, C:0.09, G:0.09, T:0.15
Consensus pattern (17 bp):
AAAATGCAATAACAAAA
Found at i:12264527 original size:21 final size:22
Alignment explanation
Indices: 12264503--12264551 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
12264493 TCATCTTCAG
*
12264503 CAACTTCT-TCTTCTTCAACAA
1 CAACTTCTCTCTTCTACAACAA
* *
12264524 CAACTT-TCTCTTCTACAGCAG
1 CAACTTCTCTCTTCTACAACAA
12264545 CAACTTC
1 CAACTTC
12264552 CTTATCAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.27, C:0.35, G:0.04, T:0.35
Consensus pattern (22 bp):
CAACTTCTCTCTTCTACAACAA
Found at i:12281356 original size:43 final size:43
Alignment explanation
Indices: 12281309--12281424 Score: 205
Period size: 43 Copynumber: 2.7 Consensus size: 43
12281299 TGTAATTTCA
12281309 TGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGAGAACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGAGAACG
* * *
12281352 TGTAAGACCATGTCTAGGACAGTGGAATCGAAGTGAGAGAACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGAGAACG
12281395 TGTAAGACCATGTCTGGGACATTGGCATCG
1 TGTAAGACCATGTCTGGGACATTGGCATCG
12281425 TATATGAGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGAGAACG
Found at i:12281420 original size:86 final size:84
Alignment explanation
Indices: 12281309--12281467 Score: 230
Period size: 84 Copynumber: 1.9 Consensus size: 84
12281299 TGTAATTTCA
*
12281309 TGTAAGACCATGTCTGGGACATTGGCATCGAAGTGA-GAGAACGTGTAAGACCATGTCTAGGACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGAA-T-ATGAG-ACGTATAAGACCATGTCTAGGACA
12281373 GTGGAATCGAAGTGAGAGAACG
63 GTGGAATCGAAGTGAGAGAACG
* * * *
12281395 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGAGTCGTATAATACCCTGTCTAGGACAGTG
1 TGTAAGACCATGTCTGGGACATTGGCATCGAATATGAGACGTATAAGACCATGTCTAGGACAGTG
*
12281460 GCATCGAA
66 GAATCGAA
12281468 ATGTGCTAAC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
84 31 0.47
85 4 0.06
86 31 0.47
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (84 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGAATATGAGACGTATAAGACCATGTCTAGGACAGTG
GAATCGAAGTGAGAGAACG
Found at i:12288679 original size:25 final size:25
Alignment explanation
Indices: 12288642--12288750 Score: 137
Period size: 25 Copynumber: 4.4 Consensus size: 25
12288632 ACTCGAAATA
* *
12288642 GAGCTTACTGATATTCAGCTTATAT
1 GAGCTTACCGATATTCAGCTCATAT
12288667 GAGCTTACCGATATTCAGCTCATAT
1 GAGCTTACCGATATTCAGCTCATAT
* **
12288692 GAGCTTACCGATATTCAGTTCGCAT
1 GAGCTTACCGATATTCAGCTCATAT
* * *
12288717 GAGCTTACCGTTACTCGGCTCATAT
1 GAGCTTACCGATATTCAGCTCATAT
*
12288742 TAGCTTACC
1 GAGCTTACC
12288751 AATTATAGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 72 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (25 bp):
GAGCTTACCGATATTCAGCTCATAT
Found at i:12288775 original size:24 final size:24
Alignment explanation
Indices: 12288748--12288795 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
12288738 ATATTAGCTT
12288748 ACCAATTATA-GCTCGTAAGAGCAG
1 ACCAATT-TAGGCTCGTAAGAGCAG
*
12288772 ACCAATTTAGGGCTCGTATGAGCA
1 ACCAATTTA-GGCTCGTAAGAGCA
12288796 TACATGTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 7 0.33
25 12 0.57
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (24 bp):
ACCAATTTAGGCTCGTAAGAGCAG
Found at i:12291394 original size:27 final size:27
Alignment explanation
Indices: 12291308--12291535 Score: 129
Period size: 28 Copynumber: 8.2 Consensus size: 27
12291298 AGATAGGCAT
**
12291308 AAAGGCTTCCTTT-TACAGAGATCACCAC
1 AAAGGCTTCCTTTATA-A-AGATTGCCAC
* ***
12291336 GAAGGCTTCCTTTA-ACAGAGATCATCAC
1 AAAGGCTTCCTTTATA-A-AGATTGCCAC
*
12291364 AAAGGCTTCCTTTATAAAGATTGCCAT
1 AAAGGCTTCCTTTATAAAGATTGCCAC
** * * * *
12291391 AAAGGCTTTATTTAACAAATATCGTCAC
1 AAAGGCTTCCTTT-ATAAAGATTGCCAC
* * *
12291419 AAAGGTTTTCTTTA-ACAGAGATTACCAC
1 AAAGGCTTCCTTTATA-A-AGATTGCCAC
* * *
12291447 AAATGCTTCCCTTATAGAGATTGCCAC
1 AAAGGCTTCCTTTATAAAGATTGCCAC
* * *
12291474 AAAGGGTTCCTTTACAAAGATTTCCAC
1 AAAGGCTTCCTTTATAAAGATTGCCAC
* *
12291501 AAAGGCATTTCTTTCTATAAGATTGCCAC
1 AAAGGC-TTCCTTTATA-AAGATTGCCAC
*
12291530 GAAGGC
1 AAAGGC
12291536 ATCCATTTTC
Statistics
Matches: 154, Mismatches: 38, Indels: 15
0.74 0.18 0.07
Matches are distributed among these distances:
26 1 0.01
27 54 0.35
28 82 0.53
29 17 0.11
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (27 bp):
AAAGGCTTCCTTTATAAAGATTGCCAC
Found at i:12291512 original size:83 final size:82
Alignment explanation
Indices: 12291308--12291514 Score: 227
Period size: 83 Copynumber: 2.5 Consensus size: 82
12291298 AGATAGGCAT
* * * * *
12291308 AAAGGCTTCCTTTTACAGAGATCACCACGAAGGCTTCCTTTAACAGAGATCATCACAAAGGCTTC
1 AAAGGCTTCC-TTTACAAAGATCTCCACAAAGGCTTTCTTTAACAGAGATCACCACAAAGGCTTC
* *
12291373 CTTTATAAAGATTGCCAT
65 CCTTATAAAGATTGCCAC
** * * * *
12291391 AAAGGCTTTATTTAACAAATATCGT-CACAAAGGTTTTCTTTAACAGAGATTACCACAAATGCTT
1 AAAGGCTTCCTTT-ACAAAGATC-TCCACAAAGGCTTTCTTTAACAGAGATCACCACAAAGGCTT
*
12291455 CCCTTATAGAGATTGCCAC
64 CCCTTATAAAGATTGCCAC
* *
12291474 AAAGGGTTCCTTTACAAAGATTTCCACAAAGGCATTTCTTT
1 AAAGGCTTCCTTTACAAAGATCTCCACAAAGGC-TTTCTTT
12291515 CTATAAGATT
Statistics
Matches: 100, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
81 1 0.01
82 18 0.18
83 81 0.81
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (82 bp):
AAAGGCTTCCTTTACAAAGATCTCCACAAAGGCTTTCTTTAACAGAGATCACCACAAAGGCTTCC
CTTATAAAGATTGCCAC
Found at i:12291529 original size:29 final size:30
Alignment explanation
Indices: 12291459--12291537 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
12291449 ATGCTTCCCT
*
12291459 TATAGAGATTGCCACAAAGG-GTTCCTTTAC
1 TATA-AGATTGCCACAAAGGCATTCCTTTAC
* *
12291489 -A-AAGATTTCCACAAAGGCATTTCTTT-C
1 TATAAGATTGCCACAAAGGCATTCCTTTAC
*
12291516 TATAAGATTGCCACGAAGGCAT
1 TATAAGATTGCCACAAAGGCAT
12291538 CCATTTTCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
27 15 0.37
28 8 0.20
29 18 0.44
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (30 bp):
TATAAGATTGCCACAAAGGCATTCCTTTAC
Found at i:12291587 original size:29 final size:29
Alignment explanation
Indices: 12291549--12291617 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
12291539 CATTTTCATT
12291549 CCTTT-TAGAGAT-TCGCCATGAAA-GCTTA
1 CCTTTCTAGAG-TCTCGCCAT-AAAGGCTTA
* *
12291577 CCTTTCTAGAGTCTTGCCATAAAGGCTTG
1 CCTTTCTAGAGTCTCGCCATAAAGGCTTA
*
12291606 CCTTTCTGGAGT
1 CCTTTCTAGAGT
12291618 TTTGTCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 9 0.26
29 26 0.74
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (29 bp):
CCTTTCTAGAGTCTCGCCATAAAGGCTTA
Found at i:12291629 original size:29 final size:29
Alignment explanation
Indices: 12291572--12291630 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
12291562 CGCCATGAAA
*
12291572 GCTTACCTTTCTAGAGTCTTGCCATAAAG
1 GCTTACCTTTCTAGAGTCTTGCCAAAAAG
* * * *
12291601 GCTTGCCTTTCTGGAGTTTTGTCAAAAAG
1 GCTTACCTTTCTAGAGTCTTGCCAAAAAG
12291630 G
1 G
12291631 TTGTCATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (29 bp):
GCTTACCTTTCTAGAGTCTTGCCAAAAAG
Found at i:12291879 original size:53 final size:52
Alignment explanation
Indices: 12291765--12291896 Score: 147
Period size: 53 Copynumber: 2.5 Consensus size: 52
12291755 TCATATGCTG
* * * ** *
12291765 CCATAACCCACCAGTTACGATCTTACAAATATGGTTTTCCTTCTATATGATG
1 CCATAACCCACCAGTTACGGTCTTACAAATATGGTCTTCCTTCCATAAAATC
* * ** *
12291817 TCATAACCCACTAGTTACGGTCTTACACGGTATGGTCTTCTTTCCATAAAATC
1 CCATAACCCACCAGTTACGGTCTTACA-AATATGGTCTTCCTTCCATAAAATC
*
12291870 CCATAACCCACCAGTTATGGTCTTACA
1 CCATAACCCACCAGTTACGGTCTTACA
12291897 TGATATAGTC
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
52 24 0.37
53 41 0.63
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (52 bp):
CCATAACCCACCAGTTACGGTCTTACAAATATGGTCTTCCTTCCATAAAATC
Found at i:12296318 original size:27 final size:27
Alignment explanation
Indices: 12296264--12296386 Score: 76
Period size: 27 Copynumber: 4.6 Consensus size: 27
12296254 ACATAAGGCC
*
12296264 ATAACAGTCATTTCATCTCCTA-GG-GGT
1 ATAACAGTCATTTTA-C-CCTATGGAGGT
*
12296291 ATAACAGTTATTTTACCCTATGGAGGT
1 ATAACAGTCATTTTACCCTATGGAGGT
** *
12296318 ATTTCAGTCATTTTATCCTAT-GAGGGT
1 ATAACAGTCATTTTACCCTATGGA-GGT
* * * *
12296345 A-ATTCAATCATTTTACCCTGTGGGGGT
1 ATA-ACAGTCATTTTACCCTATGGAGGT
*
12296372 A-ATTCAGTCATTTTA
1 ATA-ACAGTCATTTTA
12296387 TCCTGTAAGG
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
25 4 0.05
26 5 0.06
27 69 0.87
28 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (27 bp):
ATAACAGTCATTTTACCCTATGGAGGT
Found at i:12296358 original size:54 final size:54
Alignment explanation
Indices: 12296300--12296438 Score: 199
Period size: 54 Copynumber: 2.6 Consensus size: 54
12296290 TATAACAGTT
* * *
12296300 ATTTTACCCTATGGAGGTATTTCAGTCATTTTATCCTATGAGGGTAATTCAATC
1 ATTTTACCCTATGGGGGTAATTCAGTCATTTTATCCTATAAGGGTAATTCAATC
* * **
12296354 ATTTTACCCTGTGGGGGTAATTCAGTCATTTTATCCTGTAAGGGTAATTCGGTC
1 ATTTTACCCTATGGGGGTAATTCAGTCATTTTATCCTATAAGGGTAATTCAATC
12296408 ATTTTACCCTATGGGGGTAATTC-GATCATTT
1 ATTTTACCCTATGGGGGTAATTCAG-TCATTT
12296439 ATTGACCTCT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
53 1 0.01
54 75 0.99
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (54 bp):
ATTTTACCCTATGGGGGTAATTCAGTCATTTTATCCTATAAGGGTAATTCAATC
Found at i:12296391 original size:27 final size:27
Alignment explanation
Indices: 12296295--12296438 Score: 164
Period size: 27 Copynumber: 5.3 Consensus size: 27
12296285 AGGGGTATAA
* * *
12296295 CAGTTATTTTACCCTATGGAGGTATTT
1 CAGTCATTTTACCCTATGGGGGTAATT
* *
12296322 CAGTCATTTTATCCTATGAGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
* *
12296349 CAATCATTTTACCCTGTGGGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
* * **
12296376 CAGTCATTTTATCCTGTAAGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
*
12296403 CGGTCATTTTACCCTATGGGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
12296430 C-GATCATTT
1 CAG-TCATTT
12296439 ATTGACCTCT
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 97 0.99
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTAATT
Found at i:12296698 original size:20 final size:20
Alignment explanation
Indices: 12296673--12296744 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
12296663 GCCCACACAA
*
12296673 CCCATTTCGGCCCAACGTGG
1 CCCATTACGGCCCAACGTGG
*
12296693 CCCATTACAGCCCAACGTGG
1 CCCATTACGGCCCAACGTGG
*
12296713 CCTATTACGGCCCAACGTGG
1 CCCATTACGGCCCAACGTGG
*
12296733 CCTATTACGGCC
1 CCCATTACGGCC
12296745 TAAGCCCATG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.19, C:0.39, G:0.22, T:0.19
Consensus pattern (20 bp):
CCCATTACGGCCCAACGTGG
Found at i:12302531 original size:20 final size:19
Alignment explanation
Indices: 12302494--12302533 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12302484 GGAAGTATGA
*
12302494 TTTTTTATCTTATTTGAGT
1 TTTTTTATCTTATCTGAGT
*
12302513 TTTTTTATGTTATCCTGAGT
1 TTTTTTATCTTAT-CTGAGT
12302533 T
1 T
12302534 ATGGAATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.65
Consensus pattern (19 bp):
TTTTTTATCTTATCTGAGT
Found at i:12308041 original size:27 final size:28
Alignment explanation
Indices: 12308006--12308059 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
12307996 GCTGGACTTG
12308006 GACATCATTAAAAACATGTAATAAAATT
1 GACATCATTAAAAACATGTAATAAAATT
* *
12308034 GACA-CATTAATAACATGTATTAAAAT
1 GACATCATTAAAAACATGTAATAAAAT
12308060 AAAACACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (28 bp):
GACATCATTAAAAACATGTAATAAAATT
Found at i:12308872 original size:24 final size:21
Alignment explanation
Indices: 12308852--12308892 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12308842 GAAATATGCA
12308852 ATTAATTTATTAGAAAAATAT
1 ATTAATTTATTAGAAAAATAT
* *
12308873 ATTCATTTATTAGTAAAATA
1 ATTAATTTATTAGAAAAATA
12308893 AAATATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTAATTTATTAGAAAAATAT
Found at i:12309545 original size:21 final size:21
Alignment explanation
Indices: 12309503--12309545 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12309493 TAGAATACTT
* *
12309503 TTTTAGTATTTTTTTTATATA
1 TTTTAGTATTTTTTTAAAATA
12309524 TTTTAGT-TTTTTTATAAAATA
1 TTTTAGTATTTTTT-TAAAATA
12309545 T
1 T
12309546 CAAATTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTAGTATTTTTTTAAAATA
Found at i:12313582 original size:21 final size:21
Alignment explanation
Indices: 12313558--12313597 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12313548 TTATAGAAAA
*
12313558 TAAAGATGATTAATTAAAGAT
1 TAAACATGATTAATTAAAGAT
*
12313579 TAAACTTGATTAATTAAAG
1 TAAACATGATTAATTAAAG
12313598 CTAATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (21 bp):
TAAACATGATTAATTAAAGAT
Found at i:12315151 original size:49 final size:49
Alignment explanation
Indices: 12315025--12315259 Score: 128
Period size: 49 Copynumber: 4.8 Consensus size: 49
12315015 CTTAGGATCG
** * * * *
12315025 AAACCATCATTTTCAAGCCATCCAGGATGGTAAGATAT-GCAAATAGTGA
1 AAACCATCATTTTCGGGTCATCTAGGATGGTAAAATATCG-AAATAATGA
** * * *
12315074 AAACCAT--TGTTTCTAAGTCA-CTCGGGATGGTAAAATGT-GAAAATAGTGA
1 AAACCATCAT-TTTC-GGGTCATCT-AGGATGGTAAAATATCG-AAATAATGA
* *
12315123 AAACCATCATTGTT-GGGTCATCTAGGATGGTAGAATATCGAAATAATGG
1 AAACCATCATT-TTCGGGTCATCTAGGATGGTAAAATATCGAAATAATGA
** * * *
12315172 AAACCATCATTTTCGGGTCAT-TCAACATGGTAGAATATAC-AGATAGTGA
1 AAACCATCATTTTCGGGTCATCT-AGGATGGTAAAATAT-CGAAATAATGA
* * * *
12315221 AAGCCATCATTGTCGAGTCATC-CGAGATGGTAAAATATC
1 AAACCATCATTTTCGGGTCATCTAG-GATGGTAAAATATC
12315260 AAGATGTGTA
Statistics
Matches: 148, Mismatches: 25, Indels: 27
0.74 0.12 0.14
Matches are distributed among these distances:
47 1 0.01
48 9 0.06
49 130 0.88
50 5 0.03
51 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (49 bp):
AAACCATCATTTTCGGGTCATCTAGGATGGTAAAATATCGAAATAATGA
Found at i:12326570 original size:16 final size:16
Alignment explanation
Indices: 12326550--12326618 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
12326540 TTGGTTCGCT
*
12326550 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
12326566 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
* *
12326582 GTGATGGAATAGATGC
1 GTAATGGAATAGAGGC
12326598 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
12326614 GTAAT
1 GTAAT
12326619 AGGTAATTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.36, C:0.04, G:0.36, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:12326690 original size:44 final size:46
Alignment explanation
Indices: 12326604--12326696 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
12326594 ATGCGTAATG
* *
12326604 GAATAGAGGCGTAATAGGTAATTCTTTTGTTTGATTGAATGGAATA
1 GAATAGAGGCGTAATAGGTAATTATTGTGTTTGATTGAATGGAATA
*
12326650 GAATAGAGGCGTAAT-GGT-ATTATTGTGTTTGGTTGAATGGAATA
1 GAATAGAGGCGTAATAGGTAATTATTGTGTTTGATTGAATGGAATA
12326694 GAA
1 GAA
12326697 GTGTAATAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 26 0.59
45 3 0.07
46 15 0.34
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (46 bp):
GAATAGAGGCGTAATAGGTAATTATTGTGTTTGATTGAATGGAATA
Found at i:12326693 original size:39 final size:41
Alignment explanation
Indices: 12326600--12326705 Score: 108
Period size: 44 Copynumber: 2.5 Consensus size: 41
12326590 ATAGATGCGT
* *
12326600 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGATTG
1 AATGGAATAGAGGCGTAATAGGTAATTATTGTGTTTGATTG
*
12326641 AATGGAATAGAATAGAGGCGTAAT-GGT-ATTATTGTGTTTGGTTG
1 AAT-G----GAATAGAGGCGTAATAGGTAATTATTGTGTTTGATTG
* *
12326685 AATGGAATAGAAGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
12326706 CATAAGAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
39 13 0.24
40 1 0.02
41 3 0.06
42 1 0.02
43 1 0.02
44 17 0.31
45 3 0.06
46 15 0.28
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (41 bp):
AATGGAATAGAGGCGTAATAGGTAATTATTGTGTTTGATTG
Found at i:12328443 original size:15 final size:15
Alignment explanation
Indices: 12328392--12328450 Score: 82
Period size: 15 Copynumber: 3.8 Consensus size: 15
12328382 ATTTTCCAAA
12328392 AAGCATATAACAAGC
1 AAGCATATAACAAGC
* *
12328407 AAGCAACATAACATAAC
1 AAGC-ATATAACA-AGC
12328424 AAGCATATAACAAGC
1 AAGCATATAACAAGC
12328439 AAGCATATAACA
1 AAGCATATAACA
12328451 TAACATAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
15 18 0.47
16 14 0.37
17 6 0.16
ACGTcount: A:0.56, C:0.20, G:0.10, T:0.14
Consensus pattern (15 bp):
AAGCATATAACAAGC
Found at i:12328451 original size:36 final size:32
Alignment explanation
Indices: 12328392--12328497 Score: 114
Period size: 32 Copynumber: 3.4 Consensus size: 32
12328382 ATTTTCCAAA
12328392 AAGCATATAACAAGCAAGCAACATAACATAAC
1 AAGCATATAACAAGCAAGCAACATAACATAAC
*
12328424 AAGCATATAACAAGCAAGC-ATATAACATAAC
1 AAGCATATAACAAGCAAGCAACATAACATAAC
* * **
12328455 ATA--ACA-AACATAACAAATAACA-AACATAAC
1 A-AGCATATAACA-AGCAAGCAACATAACATAAC
12328485 AAGCATATAACAA
1 AAGCATATAACAA
12328498 CATAACATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
29 5 0.08
30 15 0.25
31 17 0.28
32 24 0.39
ACGTcount: A:0.59, C:0.20, G:0.07, T:0.14
Consensus pattern (32 bp):
AAGCATATAACAAGCAAGCAACATAACATAAC
Found at i:12328455 original size:5 final size:5
Alignment explanation
Indices: 12328445--12328509 Score: 57
Period size: 5 Copynumber: 13.2 Consensus size: 5
12328435 AAGCAAGCAT
*
12328445 ATAAC ATAAC ATAAC A-AAC ATAAC AAATAAC A-AAC ATAAC A-AGC ATATA-
1 ATAAC ATAAC ATAAC ATAAC ATAAC --ATAAC ATAAC ATAAC ATAAC ATA-AC
*
12328494 ACAAC ATAAC ATAAC A
1 ATAAC ATAAC ATAAC A
12328510 CTTCTCAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
4 12 0.24
5 32 0.65
7 5 0.10
ACGTcount: A:0.63, C:0.20, G:0.02, T:0.15
Consensus pattern (5 bp):
ATAAC
Found at i:12328461 original size:25 final size:25
Alignment explanation
Indices: 12328430--12328509 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 25
12328420 TAACAAGCAT
* *
12328430 ATAACAAGCA-AGCATATAACATAAC
1 ATAACAAGCATAACAAATAACA-AAC
*
12328455 ATAACAAACATAACAAATAACAAAC
1 ATAACAAGCATAACAAATAACAAAC
12328480 ATAACAAGCATATAACAACATAACATAAC
1 ATAACAAGC--ATAACAA-ATAACA-AAC
12328509 A
1 A
12328510 CTTCTCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
25 20 0.43
26 9 0.20
27 7 0.15
28 6 0.13
29 4 0.09
ACGTcount: A:0.61, C:0.20, G:0.04, T:0.15
Consensus pattern (25 bp):
ATAACAAGCATAACAAATAACAAAC
Found at i:12328496 original size:16 final size:16
Alignment explanation
Indices: 12328392--12328496 Score: 80
Period size: 16 Copynumber: 6.8 Consensus size: 16
12328382 ATTTTCCAAA
*
12328392 AAGCATATAACA-AGC
1 AAGCATATAACATAAC
*
12328407 AAGCAACATAACATAAC
1 AAGC-ATATAACATAAC
*
12328424 AAGCATATAACA-AGC
1 AAGCATATAACATAAC
12328439 AAGCATATAACATAAC
1 AAGCATATAACATAAC
*
12328455 ATA--ACA-AACATAAC
1 A-AGCATATAACATAAC
*
12328469 AA--ATAACAAACATAAC
1 AAGCAT-A-TAACATAAC
12328485 AAGCATATAACA
1 AAGCATATAACA
12328497 ACATAACATA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
13 2 0.03
14 10 0.14
15 20 0.27
16 31 0.42
17 8 0.11
18 2 0.03
ACGTcount: A:0.59, C:0.20, G:0.07, T:0.14
Consensus pattern (16 bp):
AAGCATATAACATAAC
Found at i:12329834 original size:23 final size:22
Alignment explanation
Indices: 12329802--12329846 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
12329792 TCGGAAGCAA
12329802 GAAATGAAACAGGAATAGAAAT
1 GAAATGAAACAGGAATAGAAAT
12329824 GAAAGTGAAACAGGAATAGAAAT
1 GAAA-TGAAACAGGAATAGAAAT
12329847 CGGGAGCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.58, C:0.04, G:0.24, T:0.13
Consensus pattern (22 bp):
GAAATGAAACAGGAATAGAAAT
Found at i:12335885 original size:18 final size:17
Alignment explanation
Indices: 12335850--12335895 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
12335840 TTTTTTACAT
*
12335850 TTATCTTAA-AAT-TAA
1 TTATTTTAATAATGTAA
12335865 TTAATTTTAATAATGTAA
1 TT-ATTTTAATAATGTAA
*
12335883 TTATTTTTATAAT
1 TTATTTTAATAAT
12335896 TTTCATATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 2 0.08
16 6 0.23
17 13 0.50
18 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTATTTTAATAATGTAA
Found at i:12335894 original size:17 final size:18
Alignment explanation
Indices: 12335862--12335895 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12335852 ATCTTAAAAT
12335862 TAATTAATTTTAATAATG
1 TAATTAATTTTAATAATG
*
12335880 TAATT-ATTTTTATAAT
1 TAATTAATTTTAATAAT
12335896 TTTCATATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TAATTAATTTTAATAATG
Found at i:12335916 original size:26 final size:26
Alignment explanation
Indices: 12335866--12335915 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
12335856 TAAAATTAAT
12335866 TAATTTTAATAATGTAATTATTTTTA
1 TAATTTTAATAATGTAATTATTTTTA
*
12335892 TAATTTTCAT-ATGTAATTATTTTT
1 TAATTTTAATAATGTAATTATTTTT
12335916 TTTACATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (26 bp):
TAATTTTAATAATGTAATTATTTTTA
Found at i:12348579 original size:217 final size:217
Alignment explanation
Indices: 12348204--12349098 Score: 1305
Period size: 217 Copynumber: 4.1 Consensus size: 217
12348194 ACCAATGATT
* * * * * * *
12348204 CTATCTCCCTGAAGTTGCAGTGGAGCTGATTAAAACC-ACAGATCCTATCTCTCTGAAGTTGCAG
1 CTATCTCCCTGAAGTTGAAGTGGAGCGGATTAAATCCTTC-GATCTTATCTCTCTGAAGTTACAA
* *
12348268 AGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCT
65 AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
** * *
12348333 TATCCTCCTGAAGTTATAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGT
130 TATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGATGAAGT
*
12348398 GGAACAGGTTAAAGCCGATAATC
195 GGAGCAGGTTAAAGCCGATAATC
* * * *
12348421 CTATCTCCCTGAAGTTGAAGTGGAGCGAATTAAATCCTTGGATCTTATCTCTCTGAAATTTCAAA
1 CTATCTCCCTGAAGTTGAAGTGGAGCGGATTAAATCCTTCGATCTTATCTCTCTGAAGTTACAAA
* * *
12348486 AAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGTAGTGGAGTAGACTAAGTAAGCAAGTCTT
66 GAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTT
* * *
12348551 ATCCTCCTGAAGTTGTAGTGGTGCAGACTGAAGATGGCAAACCTTATCTCCCTGAGGATGAAGTG
131 ATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGATGAAGTG
12348616 GAGCAGGTTAAAGCCGATAATC
196 GAGCAGGTTAAAGCCGATAATC
* * *
12348638 CTATC-CCCTTGAAATTGTAGTGGAGCGGATTAAATCCTTCGATCTTATCTCTCTGAAGTTACAG
1 CTATCTCCC-TGAAGTTGAAGTGGAGCGGATTAAATCCTTCGATCTTATCTCTCTGAAGTTACAA
* *
12348702 AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGCAAGCAAGTCT
65 AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
** *
12348767 TATCCTCCTGAAGTTGCAGTGATGCAGACTGAAGATGGCAAACCTTATCTCCCTGAGGATGAAGT
130 TATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGATGAAGT
*
12348832 GGAGCAGGCTAAAGCCGATAATC
195 GGAGCAGGTTAAAGCCGATAATC
* *
12348855 CTATC-CCCTTGAAATT-ACAGTGGAGAGGATTAAATCCTTCGATCTTATCTCTCTGAAGTTACA
1 CTATCTCCC-TGAAGTTGA-AGTGGAGCGGATTAAATCCTTCGATCTTATCTCTCTGAAGTTACA
*
12348918 AAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTC
64 AAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTC
* * * * *
12348983 TTATCCTCCTGAAGTTGCACTGGGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAG
129 TTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGATGAAG
* *
12349048 TGGAGCAGATTAAAAGTCGATAATC
194 TGGAGCAGGTT-AAAGCCGATAATC
*
12349073 CTATCTCCTTGAAGTTGCAA-TGGAGC
1 CTATCTCCCTGAAGTTG-AAGTGGAGC
12349099 AGACTAAGTA
Statistics
Matches: 617, Mismatches: 54, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
216 3 0.00
217 582 0.94
218 28 0.05
219 3 0.00
220 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (217 bp):
CTATCTCCCTGAAGTTGAAGTGGAGCGGATTAAATCCTTCGATCTTATCTCTCTGAAGTTACAAA
GAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTT
ATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGATGAAGTG
GAGCAGGTTAAAGCCGATAATC
Found at i:12348769 original size:44 final size:44
Alignment explanation
Indices: 12348205--12349106 Score: 252
Period size: 44 Copynumber: 20.8 Consensus size: 44
12348195 CCAATGATTC
* * * *
12348205 TATCTCCCTGAAGTTGCAGTGGAGCTGATTAA--AACCACAGATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCA-A-ATCT
* * * * * *
12348249 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGC-ATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAATCT
* * * *
12348289 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAATCT
** * * *
12348333 TATC-CTCCTGAAGTTATAGTGGGGCAGACTGAAG-ATGGCAAACCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGCA-AGCAAATCT
* ** * *
12348378 TATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAGC-CG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAAGCA-AATCT
* * ** **
12348422 TATCTCCCTGAAGTTGAAGTGGAGC-GAATTAA--ATCCTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ACTAAGCAAGC--AAATCT
* * * *** * * * *
12348466 TATCTCTCTGAAATTTCA-AAAAGCAGA-T-CGC-ATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAATCT
* * * *
12348506 TATCTCCCTGAAGTTGTAGTGGAGTAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAATCT
* * * *
12348550 TATC-CTCCTGAAGTTGTAGTGGTGCAGACTGAAG-ATGGCAAACCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGCA-AGCAAATCT
* * * ** * *
12348595 TATCTCCCTGAGGATGAAGTGGAGCAGGTTAAAGC-CG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAAGCA-AATCT
* * * * * *** *
12348639 TATC-CCCTTGAAATTGTAGTGGAGCGGATTAAATCCTTC-GATCT
1 TATCTCCC-TGAAGTTGCAGTGGAGCAGACT-AAGCAAGCAAATCT
* * * * * * *
12348683 TATCTCTCTGAAGTTACAG-AGAGCAGA-T-CGC-ATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAATCT
* *
12348723 TATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGCAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAATCT
* *
12348767 TATC-CTCCTGAAGTTGCAGT-GATGCAGACTGAAG-ATGGCAAACCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGCA-AGCAAATCT
* * * * * *
12348812 TATCTCCCTGAGGATGAAGTGGAGCAGGCTAAAGC-CG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAAGCA-AATCT
* * * * *** *
12348856 TATC-CCCTTGAAATTACAGTGGAG-AGGATTAAATCCTTC-GATCT
1 TATCTCCC-TGAAGTTGCAGTGGAGCA-GACT-AAGCAAGCAAATCT
* * ** * * * *
12348900 TATCTCTCTGAAGTTACA-AAGAGCAGA-T-CGC-ATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAATCT
* * *
12348940 TATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAATCT
* * *
12348984 TATC-CTCCTGAAGTTGCACTGGGGCAGACTAAAG-ATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGCA-AGCAAATCT
* *
12349029 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AAGTCGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAG-C-A-AATCT
* *
12349074 TATCTCCTTGAAGTTGCAATGGAGCAGACTAAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG
12349107 TAGAACAGAT
Statistics
Matches: 626, Mismatches: 166, Indels: 130
0.68 0.18 0.14
Matches are distributed among these distances:
39 4 0.01
40 76 0.12
41 26 0.04
42 12 0.02
43 47 0.08
44 283 0.45
45 172 0.27
46 6 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAATCT
Found at i:12349044 original size:45 final size:45
Alignment explanation
Indices: 12348937--12349105 Score: 177
Period size: 45 Copynumber: 3.8 Consensus size: 45
12348927 TCGCATCTAG
* * *
12348937 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACT-AAG-TAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT-GGCAAA
* *
12348981 TCTTATC-CTCCTGAAGTTGCACTGGGGCAGACTAAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACTAAAGATGGCAAA
* *
12349026 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-A-GTCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATGGC-A-AA
* * *
12349071 TCCTATCTCCTTGAAGTTGCAATGGAGCAGACTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
12349106 GTAGAACAGA
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
43 3 0.03
44 30 0.28
45 71 0.67
46 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATGGCAAA
Found at i:12351027 original size:12 final size:12
Alignment explanation
Indices: 12351010--12351056 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
12351000 TTATTCTTTA
*
12351010 TATTTTTTTGTT
1 TATTTTTTTATT
12351022 TATTTTTTTATT
1 TATTTTTTTATT
* *
12351034 TATGTTTTCATT
1 TATTTTTTTATT
*
12351046 AATTTTTTTAT
1 TATTTTTTTAT
12351057 CTTGCTCGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (12 bp):
TATTTTTTTATT
Found at i:12354268 original size:30 final size:29
Alignment explanation
Indices: 12354234--12354311 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
12354224 GCTAAGTATT
12354234 GTTCTGGAAAAAATAATTTTGACAAGATGG
1 GTTCT-GAAAAAATAATTTTGACAAGATGG
* ** *
12354264 GTTCTGAAAAAATAAATTTGACGTGATGT
1 GTTCTGAAAAAATAATTTTGACAAGATGG
* *
12354293 GTTTTGAAAAAATTATTTT
1 GTTCTGAAAAAATAATTTT
12354312 AAAAACGCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 36 0.88
30 5 0.12
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.37
Consensus pattern (29 bp):
GTTCTGAAAAAATAATTTTGACAAGATGG
Found at i:12355131 original size:23 final size:24
Alignment explanation
Indices: 12355105--12355156 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
12355095 ATTTTTTAAT
*
12355105 TTTAA-TAACGTATATATTTATTA
1 TTTAACTAAAGTATATATTTATTA
* *
12355128 TTTAATCTAAATTATATTTTTATTA
1 TTTAA-CTAAAGTATATATTTATTA
12355153 TTTA
1 TTTA
12355157 TTATAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
25 19 0.79
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTAACTAAAGTATATATTTATTA
Found at i:12355167 original size:23 final size:24
Alignment explanation
Indices: 12355115--12355172 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
12355105 TTTAATAACG
* *
12355115 TATATATTTATTATTTAATCTAAA
1 TATATTTTTATTATTTAATATAAA
*
12355139 TTATATTTTTATTATTTATTATAAA
1 -TATATTTTTATTATTTAATATAAA
12355164 -ATATTTTTA
1 TATATTTTTA
12355173 AACACATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 9 0.30
25 21 0.70
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATTTTTATTATTTAATATAAA
Found at i:12357254 original size:30 final size:30
Alignment explanation
Indices: 12357219--12357278 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
12357209 AAAAACACTT
12357219 AAATTTCTCTCTAAAATTT-TCAAAGCTCTC
1 AAATTTCTC-CTAAAATTTCTCAAAGCTCTC
*
12357249 AAATTTCTCCTTAAATTTCTCAAAGCTCTC
1 AAATTTCTCCTAAAATTTCTCAAAGCTCTC
12357279 TTTAATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (30 bp):
AAATTTCTCCTAAAATTTCTCAAAGCTCTC
Found at i:12359056 original size:18 final size:18
Alignment explanation
Indices: 12359033--12359075 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12359023 TGTCAGGTGC
*
12359033 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
12359051 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
12359069 GTTTCCT
1 GTATCCT
12359076 TTTCTCAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:12365267 original size:125 final size:124
Alignment explanation
Indices: 12365044--12365411 Score: 522
Period size: 125 Copynumber: 2.9 Consensus size: 124
12365034 TCAGGTCAAA
* * * **
12365044 CAGGAACTACTGTAGAAAAAGAGCGTTCACGTGGGAGCTTTTTTCATCAATTTTGCTGATATTAT
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGC-TTTTTCATCAATTTTGCTGACAATGC
* * * *
12365109 ATCCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAATTGTCTTCTCAAAATTATTTTTT
65 ATCTTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTA-TTTTC
* *
12365170 CAGGAACTACCGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTCATCAATTTTGCTGACAGTGCA
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTCATCAATTTTGCTGACAATGCA
** *
12365235 TCTTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCATCTTCTCAAAACTATTTTC
66 TCTTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTC
* *
12365294 CAGGAACTACTGTAAAAAAAGAGCGTCCACGTGGGAGCTTTTTCCATCAATTTTGCTAACAATGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTT-CATCAATTTTGCTGACAATGC
* * *
12365359 ATCTTGCTTGAAGC-TTTTGCGATACTATTTGTTTAGAACTGTCTTCTCAAAAT
65 ATCTTGCTTGAAGCGTTTT-TGACACTATTTGTTCAGAACTGTCTTCTCAAAAT
12365412 AAATTGAATA
Statistics
Matches: 217, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
124 49 0.23
125 132 0.61
126 36 0.17
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (124 bp):
CAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTCATCAATTTTGCTGACAATGCA
TCTTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTC
Found at i:12365617 original size:34 final size:33
Alignment explanation
Indices: 12365489--12365617 Score: 150
Period size: 34 Copynumber: 3.8 Consensus size: 33
12365479 CACAAAGTTA
* * *
12365489 TTTTAAAAAAAACTAAACCTTAATTTAATTAAT
1 TTTTTAAAAACACTAAACCCTAATTTAATTAAT
*
12365522 TTTCTTAAAAACTCTAAACCCTAATTTAATTAAT
1 TTT-TTAAAAACACTAAACCCTAATTTAATTAAT
* * * *
12365556 TTATTTTAAACCCCTAAAACCTAATTTAATTAAT
1 TT-TTTAAAAACACTAAACCCTAATTTAATTAAT
*
12365590 TTTTTAAAAAACACTAAACCCTGATTTA
1 TTTTT-AAAAACACTAAACCCTAATTTA
12365618 TTTTTTAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
33 6 0.08
34 73 0.91
35 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.40
Consensus pattern (33 bp):
TTTTTAAAAACACTAAACCCTAATTTAATTAAT
Found at i:12372087 original size:21 final size:21
Alignment explanation
Indices: 12372061--12372105 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
12372051 TGAGGCTGAT
12372061 ATGACACACCATAATTAGGAA
1 ATGACACACCATAATTAGGAA
12372082 ATGACACACCATAATTAGGAA
1 ATGACACACCATAATTAGGAA
12372103 ATG
1 ATG
12372106 GTGGATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.20
Consensus pattern (21 bp):
ATGACACACCATAATTAGGAA
Found at i:12374743 original size:9 final size:9
Alignment explanation
Indices: 12374726--12374755 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
12374716 TTAAAACAAA
*
12374726 AAGTTCCCC
1 AAGTCCCCC
12374735 AAGTCCCCC
1 AAGTCCCCC
12374744 AAGTCCCCC
1 AAGTCCCCC
12374753 AAG
1 AAG
12374756 ACTCCAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.27, C:0.47, G:0.13, T:0.13
Consensus pattern (9 bp):
AAGTCCCCC
Found at i:12380253 original size:88 final size:88
Alignment explanation
Indices: 12380104--12380381 Score: 376
Period size: 88 Copynumber: 3.1 Consensus size: 88
12380094 CTTGACGAGA
* * * *
12380104 TTATGTGATGTTTGAACATTGCTGAAAGTTAGAAGTTTAGTCAGACATATTTTATGATGAGGCAT
1 TTATGTGATGTATGAACATCGATGAAAGTTAGAAGTTTAATCAGACATATTTTATGATGAGGCAT
*
12380169 AACATGCTAGTAACTCTTGAATT
66 AACATGCTAGCAACTCTTGAATT
* * * *
12380192 TTATGTGATGTATGAACGTCGATGAAAGTTAGTAGTTCAATCAGACATATTTTATGGTGAGGCAT
1 TTATGTGATGTATGAACATCGATGAAAGTTAGAAGTTTAATCAGACATATTTTATGATGAGGCAT
*
12380257 AACATGCTAGCAACTATTGAATT
66 AACATGCTAGCAACTCTTGAATT
* * * * * *
12380280 TTATGTGATGTATAAACATCAATGAAAGTTAGGAGTTTAATTAGATATATTTTATAATGAGGCAT
1 TTATGTGATGTATGAACATCGATGAAAGTTAGAAGTTTAATCAGACATATTTTATGATGAGGCAT
* *
12380345 AACTTGTTAGCAACTCTTGAATT
66 AACATGCTAGCAACTCTTGAATT
*
12380368 TTATAGTGAAGTAT
1 TTAT-GTGATGTAT
12380382 CATGTGTCTC
Statistics
Matches: 166, Mismatches: 23, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 158 0.95
89 8 0.05
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (88 bp):
TTATGTGATGTATGAACATCGATGAAAGTTAGAAGTTTAATCAGACATATTTTATGATGAGGCAT
AACATGCTAGCAACTCTTGAATT
Found at i:12382293 original size:69 final size:69
Alignment explanation
Indices: 12382175--12382648 Score: 468
Period size: 69 Copynumber: 6.9 Consensus size: 69
12382165 AATAGCATTT
* * * * *
12382175 CTGTCATACTAAGGTTCGCAGGCGAAAAGCCGCAGCCTCCAACACAGTTAGCGTGAGCAAAGCTC
1 CTGTCACACTAAGGCTCGCAGGCGAAGAGCCGTAGCCTCCAACACAGTTAGCGAGAGCAAAGCTC
*
12382240 TCAG
66 TCAA
* * * * * *
12382244 CTATCATACTAAGGCTCGTAGGTGAAGAGCCATAGCCTCCAACATAGTTAGCGAGAGCAAAGCTC
1 CTGTCACACTAAGGCTCGCAGGCGAAGAGCCGTAGCCTCCAACACAGTTAGCGAGAGCAAAGCTC
*
12382309 CCAA
66 TCAA
* * * * * * * * * *
12382313 CTATTATACTATGGCTCGCAGGCGAAGAGTCGCAGCCTTCAATACAGTTAACGAGAGCAAAGCAC
1 CTGTCACACTAAGGCTCGCAGGCGAAGAGCCGTAGCCTCCAACACAGTTAGCGAGAGCAAAGCTC
*
12382378 CCAA
66 TCAA
* * * * * ** *
12382382 CTGCCACACTAAGGCTCGTAAGCGAAGAG-TGTAGCCTCCAACATAGTTAGTTAGAGTAAAGCTC
1 CTGTCACACTAAGGCTCGCAGGCGAAGAGCCGTAGCCTCCAACACAGTTAGCGAGAGCAAAGCTC
*
12382446 TCAG
66 TCAA
* * * *** *
12382450 TTGCCACACTAAGGCTCGTAGGCGAAGAGCTACAGCCTCCAACACAGTTAGCGAGAGCAAAACTC
1 CTGTCACACTAAGGCTCGCAGGCGAAGAGCCGTAGCCTCCAACACAGTTAGCGAGAGCAAAGCTC
*
12382515 ACAA
66 TCAA
* * * * *
12382519 TTGTTACACTAAGGCTCGCAGG-TATAGAGCCGTAGCCTCCAACACAGTTAGCGAGAACAAAGTT
1 CTGTCACACTAAGGCTCGCAGGCGA-AGAGCCGTAGCCTCCAACACAGTTAGCGAGAGCAAAGCT
12382583 CTCAA
65 CTCAA
* * *
12382588 CTGTCATACTAAGGCTCGCAGGCGAAGAGTCGCT-GCCTCCAACACAGTTAGCGAGATCAAA
1 CTGTCACACTAAGGCTCGCAGGCGAAGAGCCG-TAGCCTCCAACACAGTTAGCGAGAGCAAA
12382649 ACTCCTAGCT
Statistics
Matches: 331, Mismatches: 70, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
68 55 0.17
69 274 0.83
70 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.19
Consensus pattern (69 bp):
CTGTCACACTAAGGCTCGCAGGCGAAGAGCCGTAGCCTCCAACACAGTTAGCGAGAGCAAAGCTC
TCAA
Found at i:12382568 original size:206 final size:208
Alignment explanation
Indices: 12382182--12382673 Score: 548
Period size: 206 Copynumber: 2.4 Consensus size: 208
12382172 TTTCTGTCAT
* * * *
12382182 ACTAAGGTTCGCAGGCGAAAAGCCGC-AGCCTCCAACACAGTTAGCGTGAGCAAAGCTCTCAGCT
1 ACTAAGGCTCGCAAGCGAAGAGTCGCTAGCCTCCAACACAGTTAGCGTGAGCAAAGCTCTCAGCT
* * * * * * *
12382246 ATCATACTAAGGCTCGTAGGTGAAGAGCCATAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCC
66 ACCACACTAAGGCTCGTAGGCGAAGAGCCACAGCCTCCAACACAGTTAGCGAGAGCAAAACTCAC
* * * * * *
12382311 AACTATTATACTATGGCTCGCAGGCGAAGAGTCGCAGCCTTCAATACAGTTAACGAGAGCAAAGC
131 AACTATTACACTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAACACAGTTAACGAGAACAAAGC
12382376 ACCCAACTGCCAC
196 ACCCAACTGCCAC
* * * * *
12382389 ACTAAGGCTCGTAAGCGAAGAGT-G-TAGCCTCCAACATAGTTAG-TTAGAGTAAAGCTCTCAGT
1 ACTAAGGCTCGCAAGCGAAGAGTCGCTAGCCTCCAACACAGTTAGCGT-GAGCAAAGCTCTCAGC
* *
12382451 TGCCACACTAAGGCTCGTAGGCGAAGAGCTACAGCCTCCAACACAGTTAGCGAGAGCAAAACTCA
65 TACCACACTAAGGCTCGTAGGCGAAGAGCCACAGCCTCCAACACAGTTAGCGAGAGCAAAACTCA
* * * * *
12382516 CAATTGTTACACTAAGGCTCGCAGG-TATAGAGCCGTAGCCTCCAACACAGTTAGCGAGAACAAA
130 CAACTATTACACTAAGGCTCGCAGGCGA-AGAGCCGCAGCCTCCAACACAGTTAACGAGAACAAA
** * * *
12382580 GTTCTCAACTGTCAT
194 GCACCCAACTGCCAC
* * * *
12382595 ACTAAGGCTCGCAGGCGAAGAGTCGCT-GCCTCCAACACAGTTAGCGAGATCAAAACTC-CTAGC
1 ACTAAGGCTCGCAAGCGAAGAGTCGCTAGCCTCCAACACAGTTAGCGTGAGCAAAGCTCTC-AGC
* *
12382658 TATCACACTAGGGCTC
65 TACCACACTAAGGCTC
12382674 AGAGGTGACA
Statistics
Matches: 232, Mismatches: 46, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
205 2 0.01
206 171 0.74
207 58 0.25
208 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.19
Consensus pattern (208 bp):
ACTAAGGCTCGCAAGCGAAGAGTCGCTAGCCTCCAACACAGTTAGCGTGAGCAAAGCTCTCAGCT
ACCACACTAAGGCTCGTAGGCGAAGAGCCACAGCCTCCAACACAGTTAGCGAGAGCAAAACTCAC
AACTATTACACTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAACACAGTTAACGAGAACAAAGC
ACCCAACTGCCAC
Found at i:12382666 original size:138 final size:137
Alignment explanation
Indices: 12382175--12382673 Score: 522
Period size: 138 Copynumber: 3.6 Consensus size: 137
12382165 AATAGCATTT
* * * * *
12382175 CTGTCATACTAAGGTTCGCAGGCGAAAAGCCGCAGCCTCCAACACAGTTAGCGTGAGCAAAGCT-
1 CTGTCATACTAAGGCTCGCAGGCGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAACTC
* * * *
12382239 CTCAGCTATCATACTAAGGCTCGTAGGTGAAGAGCCATAGCCTCCAACATAGTTAGCGAGAGCAA
66 CT-AACTATCACACTAAGGCTCGAAGGT-AAGAGCCGTAGCCTCCAACATAGTTAGCGAGAGCAA
*
12382304 AGCTCCCAA
129 AGCTCTCAA
* * * * * * * *
12382313 CTATTATACTATGGCTCGCAGGCGAAGAGTCGCAGCCTTCAATACAGTTAACGAGAGCAAAGCAC
1 CTGTCATACTAAGGCTCGCAGGCGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAACTC
* ** * ** *
12382378 CCAACTGCCACACTAAGGCTCGTAAGCG-AAGAG-TGTAGCCTCCAACATAGTTAGTTAGAGTAA
66 CTAACTATCACACTAAGGCTCG-AAG-GTAAGAGCCGTAGCCTCCAACATAGTTAGCGAGAGCAA
*
12382441 AGCTCTCAG
129 AGCTCTCAA
* * * * *
12382450 TTGCCACACTAAGGCTCGTAGGCGAAGAG-CTACAGCCTCCAACACAGTTAGCGAGAGCAAAACT
1 CTGTCATACTAAGGCTCGCAGGCGAAGAGTC-GCAGCCTCCAACACAGTTAGCGAGAGCAAAACT
* * * * * *
12382514 CAC-AATTGTTACACTAAGGCTCGCAGGTATAGAGCCGTAGCCTCCAACACAGTTAGCGAGAACA
65 C-CTAACTATCACACTAAGGCTCGAAGGTA-AGAGCCGTAGCCTCCAACATAGTTAGCGAGAGCA
*
12382578 AAGTTCTCAA
128 AAGCTCTCAA
* *
12382588 CTGTCATACTAAGGCTCGCAGGCGAAGAGTCGCTGCCTCCAACACAGTTAGCGAGATCAAAACTC
1 CTGTCATACTAAGGCTCGCAGGCGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAACTC
* *
12382653 CTAGCTATCACACTAGGGCTC
66 CTAACTATCACACTAAGGCTC
12382674 AGAGGTGACA
Statistics
Matches: 290, Mismatches: 61, Indels: 20
0.78 0.16 0.05
Matches are distributed among these distances:
135 1 0.00
136 4 0.01
137 104 0.36
138 176 0.61
139 4 0.01
140 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (137 bp):
CTGTCATACTAAGGCTCGCAGGCGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAACTC
CTAACTATCACACTAAGGCTCGAAGGTAAGAGCCGTAGCCTCCAACATAGTTAGCGAGAGCAAAG
CTCTCAA
Found at i:12394478 original size:30 final size:30
Alignment explanation
Indices: 12394444--12394542 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
12394434 CACTATTTTG
12394444 TATGAGTCATAAAAGTAAGTTTGTTTGTTA
1 TATGAGTCATAAAAGTAAGTTTGTTTGTTA
*
12394474 TATGAGTCATAAAAGTGAGTTTGTTTGTTAGAAAAA
1 TATGAGTCATAAAAGTAAGTTTGTTTGTT------A
12394510 GGTATGAGTCATAAAAGTAAGTTTGTTTGTTA
1 --TATGAGTCATAAAAGTAAGTTTGTTTGTTA
12394542 T
1 T
12394543 GTAAAGGAGA
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
30 29 0.49
32 1 0.02
36 1 0.02
38 28 0.47
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.40
Consensus pattern (30 bp):
TATGAGTCATAAAAGTAAGTTTGTTTGTTA
Found at i:12397528 original size:40 final size:40
Alignment explanation
Indices: 12397444--12397537 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
12397434 CTATGTTTAG
* *
12397444 CACTTAGTGTGCGATTCGAGATAACTTCAGCTATTTATGG
1 CACTTAGTGTGCGATTCGAGATAACTTCAACTATTTATGA
* **
12397484 CACTTAGTGTGCGATTGGCA-ATAGTTTCAACTATATT-TGA
1 CACTTAGTGTGCGATTCG-AGATAACTTCAACTAT-TTATGA
12397524 CACTTAGTGTGCGA
1 CACTTAGTGTGCGA
12397538 GACTGAGATA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 44 0.94
41 3 0.06
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (40 bp):
CACTTAGTGTGCGATTCGAGATAACTTCAACTATTTATGA
Found at i:12405578 original size:15 final size:15
Alignment explanation
Indices: 12405558--12405597 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
12405548 TTAAAAGAAT
12405558 TTGAAGAATCTCCTA
1 TTGAAGAATCTCCTA
*
12405573 TTGAAGAATCTCTTA
1 TTGAAGAATCTCCTA
12405588 TTGAAGAATC
1 TTGAAGAATC
12405598 ATCTTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (15 bp):
TTGAAGAATCTCCTA
Found at i:12409593 original size:30 final size:30
Alignment explanation
Indices: 12409559--12409681 Score: 174
Period size: 30 Copynumber: 3.9 Consensus size: 30
12409549 ATTTTGTATA
12409559 AGTCATAAAAGTAAGTTTGTTTGTTATATG
1 AGTCATAAAAGTAAGTTTGTTTGTTATATG
*
12409589 AGTCATAAAAGTAAGTTTTTTTGTTATAAAGGTACG
1 AGTCATAAAAGTAAGTTTGTTTGTTAT--A--T--G
*
12409625 AGTCAAAAAAGTAAGTTTGTTTGTTATATG
1 AGTCATAAAAGTAAGTTTGTTTGTTATATG
12409655 AGTCATAAAAGTAAGTTTGTTTGTTAT
1 AGTCATAAAAGTAAGTTTGTTTGTTAT
12409682 GTAAAGGAGA
Statistics
Matches: 83, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
30 53 0.64
32 2 0.02
34 2 0.02
36 26 0.31
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (30 bp):
AGTCATAAAAGTAAGTTTGTTTGTTATATG
Found at i:12415975 original size:16 final size:18
Alignment explanation
Indices: 12415948--12415982 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
12415938 TTATAAAAGT
12415948 ATAATAAAATA-TTAAAA
1 ATAATAAAATATTTAAAA
12415965 ATAAT-AAATATTTAAAA
1 ATAATAAAATATTTAAAA
12415982 A
1 A
12415983 AAACACATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATAAAATATTTAAAA
Found at i:12419347 original size:9 final size:9
Alignment explanation
Indices: 12419333--12419381 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
12419323 TTTGGTTAAA
12419333 AATTAACCG
1 AATTAACCG
12419342 AATTAACCG
1 AATTAACCG
* *
12419351 AATTACCCT
1 AATTAACCG
*
12419360 AATTAATCG
1 AATTAACCG
12419369 AATTAACCG
1 AATTAACCG
12419378 AATT
1 AATT
12419382 GAATCACTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:12419420 original size:26 final size:26
Alignment explanation
Indices: 12419389--12419440 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
12419379 ATTGAATCAC
12419389 TACATAATTAAAAACATTACATAAGT
1 TACATAATTAAAAACATTACATAAGT
*
12419415 TACATAATTAAAAACATTATATAAGT
1 TACATAATTAAAAACATTACATAAGT
12419441 CTTGAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (26 bp):
TACATAATTAAAAACATTACATAAGT
Found at i:12422225 original size:56 final size:56
Alignment explanation
Indices: 12422148--12422428 Score: 261
Period size: 56 Copynumber: 5.0 Consensus size: 56
12422138 AATTTTCAAT
* * * * *
12422148 AGCATAATAATGCTTACTTTGAGACATTGAAGCAACA-CTTTAATTTAATTTAGGAC
1 AGCATAATAATGCTCAATTTGAAACATT-AAACAACAGCTTTAATTTAATTTAAGAC
* *
12422204 AGCATAATAATACTCAATTTGAAACATTAAACATCAGC-TTAATTTAATTTAAGAC
1 AGCATAATAATGCTCAATTTGAAACATTAAACAACAGCTTTAATTTAATTTAAGAC
* * * * *
12422259 AGCATGAA-AATGCTCAATTTGATACACTAAAACACCAGCTTTAATTCAATTTATGAC
1 AGCAT-AATAATGCTCAATTTGAAACA-TTAAACAACAGCTTTAATTTAATTTAAGAC
* * * * *
12422316 AGTATGAA-AATGCTC-ATTTGAAACACTAAAACAACAGC-TTCATTCAATTTAAGAT
1 AGCAT-AATAATGCTCAATTTGAAACA-TTAAACAACAGCTTTAATTTAATTTAAGAC
* * * *
12422371 AGTATGAA-AATGCTCAATTTGAAACACTCAAACAACAGCTTTAATTCAATTTATGAC
1 AGCAT-AATAATGCTCAATTTGAAACA-TTAAACAACAGCTTTAATTTAATTTAAGAC
12422428 A
1 A
12422429 ATGCAAACAG
Statistics
Matches: 196, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
55 72 0.37
56 80 0.41
57 44 0.22
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (56 bp):
AGCATAATAATGCTCAATTTGAAACATTAAACAACAGCTTTAATTTAATTTAAGAC
Found at i:12422263 original size:55 final size:57
Alignment explanation
Indices: 12422180--12422428 Score: 312
Period size: 55 Copynumber: 4.5 Consensus size: 57
12422170 GACATTGAAG
* * * *
12422180 CAACA-CTTTAATTTAATTTAGGACAGCAT-AATAATACTCAATTTGAAACA-TTAAA
1 CAACAGCTTTAATTCAATTTAAGACAGCATGAA-AATGCTCAATTTGAAACACTAAAA
* * *
12422235 CATCAGC-TTAATTTAATTTAAGACAGCATGAAAATGCTCAATTTGATACACTAAAA
1 CAACAGCTTTAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACTAAAA
* * *
12422291 CACCAGCTTTAATTCAATTTATGACAGTATGAAAATGCTC-ATTTGAAACACTAAAA
1 CAACAGCTTTAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACTAAAA
* * * *
12422347 CAACAGC-TTCATTCAATTTAAGATAGTATGAAAATGCTCAATTTGAAACACTCAAA
1 CAACAGCTTTAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACTAAAA
*
12422403 CAACAGCTTTAATTCAATTTATGACA
1 CAACAGCTTTAATTCAATTTAAGACA
12422429 ATGCAAACAG
Statistics
Matches: 170, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
55 70 0.41
56 56 0.33
57 44 0.26
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (57 bp):
CAACAGCTTTAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACTAAAA
Found at i:12422365 original size:112 final size:112
Alignment explanation
Indices: 12422180--12422428 Score: 342
Period size: 112 Copynumber: 2.2 Consensus size: 112
12422170 GACATTGAAG
* * * *
12422180 CAACA-CTTTAATTTAATTTAGGACAGCATAATAATACTCAATTTGAAACATTAAACATCAGCTT
1 CAACAGCTTTAATTCAATTTATGACAGCATAATAATACTCAATTTGAAACATAAAACAACAGCTT
* *
12422244 AATTTAATTTAAGACAGCATGAAAATGCTCAATTTGATACACTAAAA
66 AATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACTAAAA
* * *
12422291 CACCAGCTTTAATTCAATTTATGACAGTATGAA-AATGCTC-ATTTGAAACACTAAAACAACAGC
1 CAACAGCTTTAATTCAATTTATGACAGCAT-AATAATACTCAATTTGAAACA-TAAAACAACAGC
* * * *
12422354 TTCATTCAATTTAAGATAGTATGAAAATGCTCAATTTGAAACACTCAAA
64 TTAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACTAAAA
12422403 CAACAGCTTTAATTCAATTTATGACA
1 CAACAGCTTTAATTCAATTTATGACA
12422429 ATGCAAACAG
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
111 14 0.12
112 105 0.87
113 2 0.02
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (112 bp):
CAACAGCTTTAATTCAATTTATGACAGCATAATAATACTCAATTTGAAACATAAAACAACAGCTT
AATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACTAAAA
Found at i:12423650 original size:19 final size:19
Alignment explanation
Indices: 12423626--12423664 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12423616 AAGAAAAATT
*
12423626 AGAGAAAAAGATGAGAAAA
1 AGAGAAAAAGAAGAGAAAA
12423645 AGAGAAAAAGAAGAGAAAA
1 AGAGAAAAAGAAGAGAAAA
12423664 A
1 A
12423665 TTTGTGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (19 bp):
AGAGAAAAAGAAGAGAAAA
Found at i:12423811 original size:18 final size:19
Alignment explanation
Indices: 12423790--12423836 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
12423780 ATGATTGAGA
12423790 TGGGTTGGGTAATTGGG-T
1 TGGGTTGGGTAATTGGGTT
* *
12423808 TGGGTTGGATACTTGGGTT
1 TGGGTTGGGTAATTGGGTT
*
12423827 TGGATTGGGT
1 TGGGTTGGGT
12423837 TTAGGTGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.11, C:0.02, G:0.47, T:0.40
Consensus pattern (19 bp):
TGGGTTGGGTAATTGGGTT
Found at i:12424311 original size:32 final size:30
Alignment explanation
Indices: 12424275--12424348 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 30
12424265 TACAAAATAA
*
12424275 TATTTTATATTAAATTATATTAAAAGATTTTT
1 TATTTTATATTAAATTAT-TTAAAAGA-TCTT
*
12424307 TATTTTTATATTAAATTATTTAAAATATCTT
1 TA-TTTTATATTAAATTATTTAAAAGATCTT
*
12424338 CATTTTATATT
1 TATTTTATATT
12424349 TTTCTAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 9 0.24
31 4 0.11
32 9 0.24
33 16 0.42
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (30 bp):
TATTTTATATTAAATTATTTAAAAGATCTT
Found at i:12427726 original size:25 final size:25
Alignment explanation
Indices: 12427654--12427728 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 25
12427644 GTCCAGTGAT
* * *
12427654 ATGGATCTCCGGAGCTTCCCGATTA
1 ATGGCTCTACGGAGCTTCTCGATTA
* * *
12427679 AAGGCTCTTTCATGAGCTTCTCGATTA
1 ATGGCTC-TAC-GGAGCTTCTCGATTA
12427706 ATGGCTCTACGGAGCTTCTCGAT
1 ATGGCTCTACGGAGCTTCTCGAT
12427729 ATTAGCTCGC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 17 0.43
26 4 0.10
27 19 0.47
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (25 bp):
ATGGCTCTACGGAGCTTCTCGATTA
Found at i:12427793 original size:24 final size:24
Alignment explanation
Indices: 12427766--12427835 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 24
12427756 TGGCTTGTAT
* *
12427766 GAGCTTTCCATTAATGGCTCCCCG
1 GAGCTTTCCATTAATGGCTCACAG
* *
12427790 GAGC-TTCACGTTACATGGCTCACAT
1 GAGCTTTC-CATTA-ATGGCTCACAG
*
12427815 GAGCTTTCCATTTATGTGCTC
1 GAGCTTTCCATTAATG-GCTC
12427836 GTATGAGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
23 3 0.08
24 11 0.31
25 19 0.53
26 3 0.08
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.33
Consensus pattern (24 bp):
GAGCTTTCCATTAATGGCTCACAG
Found at i:12430408 original size:19 final size:19
Alignment explanation
Indices: 12430386--12430433 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
12430376 TATTTTTATA
12430386 TTTTTTTCTTTCTTCTTCT-
1 TTTTTTTCTTT-TTCTTCTC
*
12430405 TTTTTTTCTTTTTTTTCTC
1 TTTTTTTCTTTTTCTTCTC
*
12430424 TTTTTCTCTT
1 TTTTTTTCTT
12430434 AATACAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTCTTTTTCTTCTC
Found at i:12430415 original size:9 final size:9
Alignment explanation
Indices: 12430386--12430433 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
12430376 TATTTTTATA
12430386 TTTTTTTCT
1 TTTTTTTCT
*
12430395 TTCTTCTTCT
1 TT-TTTTTCT
12430405 TTTTTTTCT
1 TTTTTTTCT
12430414 TTTTTTTCT
1 TTTTTTTCT
*
12430423 CTTTTTCTCT
1 -TTTTTTTCT
12430433 T
1 T
12430434 AATACAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:12431127 original size:30 final size:30
Alignment explanation
Indices: 12431086--12431280 Score: 156
Period size: 29 Copynumber: 6.6 Consensus size: 30
12431076 AAAACTTCTG
* *
12431086 GGGTAAAAATAT-AATTTTAGGAAAAATTAA
1 GGGTCAAAATATAAATTTTA-GAAAAGTTAA
* ** *
12431116 GGGCCAAAATATAAATAGTA-AAAAGTTAG
1 GGGTCAAAATATAAATTTTAGAAAAGTTAA
*
12431145 GGGTCAAAATGT-AATTTTAGGAAAAGTT--
1 GGGTCAAAATATAAATTTTA-GAAAAGTTAA
* * *
12431173 GGGCCCAAAATGTAAATATTA-AAAAGTTAA
1 GGG-TCAAAATATAAATTTTAGAAAAGTTAA
*
12431203 GGGTTAAAATATAAATTTTA-AAAAGTTAA
1 GGGTCAAAATATAAATTTTAGAAAAGTTAA
*
12431232 GGGGTCAAAATATAAATTTT-TAAAAGTTAA
1 -GGGTCAAAATATAAATTTTAGAAAAGTTAA
* *
12431262 GTGGT-AACATGTAAATTTT
1 G-GGTCAAAATATAAATTTT
12431281 TTTATCAAAT
Statistics
Matches: 136, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
28 15 0.11
29 60 0.44
30 56 0.41
31 5 0.04
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.30
Consensus pattern (30 bp):
GGGTCAAAATATAAATTTTAGAAAAGTTAA
Found at i:12431160 original size:59 final size:59
Alignment explanation
Indices: 12431085--12431248 Score: 201
Period size: 59 Copynumber: 2.8 Consensus size: 59
12431075 CAAAACTTCT
*
12431085 GGGGTAAAAATATAATTTTAGGAAAAATTAAGGGCCAAAATATAAATAGTAAAAAGTTA
1 GGGGTAAAAATATAATTTTAGGAAAAGTTAAGGGCCAAAATATAAATAGTAAAAAGTTA
* * * *
12431144 GGGGTCAAAATGTAATTTTAGGAAAAGTT--GGGCCCAAAATGTAAATATTAAAAAGTTA
1 GGGGTAAAAATATAATTTTAGGAAAAGTTAAGGG-CCAAAATATAAATAGTAAAAAGTTA
* * *
12431202 AGGGTTAAAATATAAATTTTA--AAAAGTTAAGGGGTCAAAATATAAAT
1 GGGGTAAAAATAT-AATTTTAGGAAAAGTTAA-GGGCCAAAATATAAAT
12431249 TTTTAAAAGT
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
57 10 0.11
58 33 0.37
59 44 0.49
60 3 0.03
ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27
Consensus pattern (59 bp):
GGGGTAAAAATATAATTTTAGGAAAAGTTAAGGGCCAAAATATAAATAGTAAAAAGTTA
Found at i:12431277 original size:59 final size:58
Alignment explanation
Indices: 12431107--12431280 Score: 187
Period size: 59 Copynumber: 3.0 Consensus size: 58
12431097 TAATTTTAGG
* *
12431107 AAAAA-TTAA-GGGCCAAAATATAAATAGTAAAAAGTTAGGGGTCAAAATGT-AATTTT
1 AAAAAGTTAAGGGGCCAAAATATAAATATTAAAAAGTTAAGGGT-AAAATGTAAATTTT
* * *
12431163 AGGAAAAGTT--GGGCCCAAAATGTAAATATTAAAAAGTTAAGGGTTAAAATATAAATTTT
1 A--AAAAGTTAAGGGGCCAAAATATAAATATTAAAAAGTTAAGGG-TAAAATGTAAATTTT
* * * *
12431222 AAAAAGTTAAGGGGTCAAAATATAAATTTTTAAAAGTTAAGTGGTAACATGTAAATTTT
1 AAAAAGTTAAGGGGCCAAAATATAAATATTAAAAAGTTAAG-GGTAAAATGTAAATTTT
12431281 TTTATCAAAT
Statistics
Matches: 97, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
56 1 0.01
57 7 0.07
58 38 0.39
59 49 0.51
60 2 0.02
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.30
Consensus pattern (58 bp):
AAAAAGTTAAGGGGCCAAAATATAAATATTAAAAAGTTAAGGGTAAAATGTAAATTTT
Found at i:12431524 original size:77 final size:76
Alignment explanation
Indices: 12431441--12431771 Score: 343
Period size: 77 Copynumber: 4.3 Consensus size: 76
12431431 TTTTTTTATT
**
12431441 TTTTTTGAAAAATAGAAATTGAAAATACCTCGGCGTGCGAACCGTGGCTCAACTCACCTCTCGGA
1 TTTTTTGAAAAATAGAAATTGAAAATACCTCGGCGTGCGAACCGAAGCTCAACTCACCTCTCGGA
12431506 TTATGAGTTGA
66 TTATGAGTTGA
* ** * ** *
12431517 TTTTTTTGAAAAATAAAAATTGATCATACCTCGGCGTGCGACCCGAAAATCAACTCATCTCTCGG
1 -TTTTTTGAAAAATAGAAATTGAAAATACCTCGGCGTGCGAACCGAAGCTCAACTCACCTCTCGG
*
12431582 ATTGTGAGTTGA
65 ATTATGAGTTGA
* * * * *
12431594 -TCTTTG-AAAACAGAAATAGAAAATTTACCTCGGCGTGC-AACCCAAAGCTCAACTCACCTATC
1 TTTTTTGAAAAATAGAAATTGAAAA--TACCTCGGCGTGCGAA-CCGAAGCTCAACTCACCTCTC
*
12431656 GGATTATGGGTT-A
63 GGATTATGAGTTGA
* * * *
12431669 -GTTTTGAGAAAATAGAAATTGAGAATATACCTCGGCGTGCG-ACCAGATGCTAAACTCACCTTT
1 TTTTTTGA-AAAATAGAAATTGA-AA-ATACCTCGGCGTGCGAACC-GAAGCTCAACTCACCTCT
12431732 CGGATTATGAGTTGA
62 CGGATTATGAGTTGA
* *
12431747 TTTCTTGAAAAA-AAAAATTGAAAAT
1 TTTTTTGAAAAATAGAAATTGAAAAT
12431772 GATTTTTGAA
Statistics
Matches: 207, Mismatches: 36, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
74 12 0.06
75 13 0.06
76 43 0.21
77 126 0.61
78 7 0.03
79 6 0.03
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (76 bp):
TTTTTTGAAAAATAGAAATTGAAAATACCTCGGCGTGCGAACCGAAGCTCAACTCACCTCTCGGA
TTATGAGTTGA
Found at i:12431735 original size:153 final size:151
Alignment explanation
Indices: 12431444--12431771 Score: 369
Period size: 153 Copynumber: 2.1 Consensus size: 151
12431434 TTTTATTTTT
*** *
12431444 TTTGAAAAATAGAAATTGAAAA-TACCTCGGCGTGCGAACCGTGGCTCAACTCACCTCTCGGATT
1 TTTGAAAAA-AGAAATTGAAAATTACCTCGGCGTGCGAACCAAAGCTCAACTCACCTATCGGATT
* * *
12431508 ATGAGTTGATTTTTTTGAAAAATAAAAATTGATCATACCTCGGCGTGCGACCCGAAAATCAACTC
65 ATGAGTTGA-TGTTTTGAAAAATAAAAATTGATCATACCTCGGCGTGCGACCAGAAAATAAACTC
* *
12431573 ATCTCTCGGATTGTGAGTTGATC
129 ACCTCTCGGATTATGAGTTGATC
* *
12431596 TTTGAAAACAGAAATAGAAAATTTACCTCGGCGTGC-AACCCAAAGCTCAACTCACCTATCGGAT
1 TTTGAAAAAAGAAATTGAAAA-TTACCTCGGCGTGCGAA-CCAAAGCTCAACTCACCTATCGGAT
* * ***
12431660 TATGGGTT-A-GTTTTGAGAAAATAGAAATTGAGAAT-ATACCTCGGCGTGCGACCAGATGCTAA
64 TATGAGTTGATGTTTTGA-AAAATAAAAATT--G-ATCATACCTCGGCGTGCGACCAGAAAATAA
* *
12431722 ACTCACCTTTCGGATTATGAGTTGATT
125 ACTCACCTCTCGGATTATGAGTTGATC
*
12431749 TCTTGAAAAAAAAAATTGAAAAT
1 T-TTGAAAAAAGAAATTGAAAAT
12431772 GATTTTTGAA
Statistics
Matches: 147, Mismatches: 21, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
150 6 0.04
151 22 0.15
152 11 0.07
153 89 0.61
154 19 0.13
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (151 bp):
TTTGAAAAAAGAAATTGAAAATTACCTCGGCGTGCGAACCAAAGCTCAACTCACCTATCGGATTA
TGAGTTGATGTTTTGAAAAATAAAAATTGATCATACCTCGGCGTGCGACCAGAAAATAAACTCAC
CTCTCGGATTATGAGTTGATC
Found at i:12438246 original size:50 final size:50
Alignment explanation
Indices: 12438191--12438291 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
12438181 GTTGGATGGA
12438191 CAGAATAAACCCTTTTTAACCATCATCT-TCTATACCTTCCGCAAAGGCGT
1 CAGAATAAACCCTTTTTAACCATCATCTGTC-ATACCTTCCGCAAAGGCGT
* * *
12438241 CAGAATAAATCCTTTTTAACGATCATCTGTCATACCTTCCGCAACGGCGT
1 CAGAATAAACCCTTTTTAACCATCATCTGTCATACCTTCCGCAAAGGCGT
12438291 C
1 C
12438292 CTTACTTTGC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 45 0.96
51 2 0.04
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.30
Consensus pattern (50 bp):
CAGAATAAACCCTTTTTAACCATCATCTGTCATACCTTCCGCAAAGGCGT
Found at i:12443752 original size:19 final size:19
Alignment explanation
Indices: 12443730--12443768 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12443720 AGAAATTTGA
*
12443730 TTTGAAAATATGAATTTTT
1 TTTGAAAATATCAATTTTT
**
12443749 TTTGAATTTATCAATTTTT
1 TTTGAAAATATCAATTTTT
12443768 T
1 T
12443769 GAAGGGCGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (19 bp):
TTTGAAAATATCAATTTTT
Found at i:12444292 original size:5 final size:5
Alignment explanation
Indices: 12444282--12444307 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12444272 CGACTGATAC
12444282 CGGGT CGGGT CGGGT CGGGT CGGGT C
1 CGGGT CGGGT CGGGT CGGGT CGGGT C
12444308 AGACCCGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.58, T:0.19
Consensus pattern (5 bp):
CGGGT
Found at i:12444381 original size:12 final size:11
Alignment explanation
Indices: 12444327--12444381 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
12444317 GTTTTTTATA
12444327 TTTT-TTCTTT
1 TTTTCTTCTTT
* *
12444337 TTTCCTTCCTT
1 TTTTCTTCTTT
*
12444348 TCTTCTTCTTT
1 TTTTCTTCTTT
12444359 TTTTCTCTCTTT
1 TTTTCT-TCTTT
12444371 TTTCTCTTCTT
1 TTT-TCTTCTT
12444382 CCCTCAATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 3 0.08
11 18 0.50
12 12 0.33
13 3 0.08
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTCTTCTTT
Found at i:12444490 original size:12 final size:11
Alignment explanation
Indices: 12444463--12444504 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
12444453 CTCCTTTCTC
12444463 TCTTTCTCCTT
1 TCTTTCTCCTT
*
12444474 TCTTTTTCCTCT
1 TCTTTCTCCT-T
12444486 TCTTTCT-CTT
1 TCTTTCTCCTT
12444496 TCTCTTCTC
1 TCT-TTCTC
12444505 TCATTCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.15
11 15 0.58
12 7 0.27
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (11 bp):
TCTTTCTCCTT
Found at i:12444492 original size:16 final size:15
Alignment explanation
Indices: 12444461--12444516 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 15
12444451 TCCTCCTTTC
12444461 TCTCTTTCTC--CTT
1 TCTCTTTCTCTTCTT
*
12444474 TCTTTTTCCTCTTCTT
1 TCTCTTT-CTCTTCTT
12444490 TCTCTTTCTCTTC--
1 TCTCTTTCTCTTCTT
*
12444503 TCTCATTCTCTTCT
1 TCTCTTTCTCTTCT
12444517 ATTTCGAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
13 18 0.50
14 3 0.08
15 6 0.17
16 9 0.25
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTCTTTCTCTTCTT
Found at i:12444686 original size:10 final size:11
Alignment explanation
Indices: 12444665--12444690 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12444655 TTGTTATTTC
12444665 TTTGGTTTTTT
1 TTTGGTTTTTT
12444676 TTTGGTTTTTT
1 TTTGGTTTTTT
12444687 TTTG
1 TTTG
12444691 CTTGGCTCTT
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:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (11 bp):
TTTGGTTTTTT
Found at i:12445099 original size:29 final size:32
Alignment explanation
Indices: 12445066--12445151 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 32
12445056 TAATTTTAGG
12445066 AAAAGTTGA-GGC-CT-AAAATATAAATAGTA
1 AAAAGTTGAGGGCGCTCAAAATATAAATAGTA
* **
12445095 AAAAGTT-AGGGCGGTCAAAATATAAATTTTA
1 AAAAGTTGAGGGCGCTCAAAATATAAATAGTA
* *
12445126 AAAAGTTGAAGG-G-TCAAAATGTAAAT
1 AAAAGTTGAGGGCGCTCAAAATATAAAT
12445152 TTTAGATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 10 0.21
30 13 0.27
31 21 0.44
32 3 0.06
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.26
Consensus pattern (32 bp):
AAAAGTTGAGGGCGCTCAAAATATAAATAGTA
Found at i:12445143 original size:30 final size:31
Alignment explanation
Indices: 12445080--12445155 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
12445070 GTTGAGGCCT
** *
12445080 AAAATATAAATAGTAAAAAGTTAGGGCGGTC
1 AAAATATAAATTTTAAAAAGTTAGAGCGGTC
12445111 AAAATATAAATTTTAAAAAGTT-GAAG-GGTC
1 AAAATATAAATTTTAAAAAGTTAG-AGCGGTC
*
12445141 AAAATGTAAATTTTA
1 AAAATATAAATTTTA
12445156 GATTTTTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 19 0.47
31 21 0.52
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.29
Consensus pattern (31 bp):
AAAATATAAATTTTAAAAAGTTAGAGCGGTC
Found at i:12445199 original size:14 final size:14
Alignment explanation
Indices: 12445170--12445218 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
12445160 TTTGTATTTT
*
12445170 TTATT-TTATT-TT
1 TTATTATTATTCTA
12445182 TTATTATTATTCTA
1 TTATTATTATTCTA
12445196 TTATTATTATTCTA
1 TTATTATTATTCTA
12445210 TTATTATTA
1 TTATTATTA
12445219 ACATGAAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 5 0.15
13 5 0.15
14 24 0.71
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTATTATTCTA
Found at i:12451482 original size:24 final size:25
Alignment explanation
Indices: 12451429--12451476 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12451419 TTGGCTCTCA
* *
12451429 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATAGCTCTTG
12451454 CGAGCTTCCCGTTA-ATAGCTCTT
1 CGAGCTTCCCGTTATATAGCTCTT
12451477 TGGAGCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.38
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGCTCTTG
Found at i:12458457 original size:52 final size:52
Alignment explanation
Indices: 12458396--12458565 Score: 241
Period size: 52 Copynumber: 3.1 Consensus size: 52
12458386 TATTGGTTTA
12458396 ACAAGTTTCATTTGAAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCT
1 ACAAGTTTCATTTGAAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCT
12458448 ACAAGTTTCATTTGAAGTTTTGACAAAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCT
1 ACAAGTTTC------A--TTTG---AAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCT
12458511 ACAAGTTTCATTTGAAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCT
1 ACAAGTTTCATTTGAAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCT
12458563 ACA
1 ACA
12458566 TACTGCAATG
Statistics
Matches: 107, Mismatches: 0, Indels: 22
0.83 0.00 0.17
Matches are distributed among these distances:
52 50 0.47
55 4 0.04
57 1 0.01
58 1 0.01
60 4 0.04
63 47 0.44
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (52 bp):
ACAAGTTTCATTTGAAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCT
Found at i:12458482 original size:63 final size:63
Alignment explanation
Indices: 12458410--12458537 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
12458400 GTTTCATTTG
12458410 AAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCTACAAGTTTCATTTGAAGTTTTGACA
1 AAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCTACAAGTTTCATTTGAAGTTTTGACA
12458473 AAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCTACAAGTTTCATTTGAAGTTTTGACA
1 AAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCTACAAGTTTCATTTGAAGTTTTGACA
12458536 AA
1 AA
12458538 AAGAATTGCT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (63 bp):
AAGTTTTGACAAAAAGAATTGCTATCAATTACTGATCTACAAGTTTCATTTGAAGTTTTGACA
Found at i:12458586 original size:52 final size:51
Alignment explanation
Indices: 12458478--12458586 Score: 132
Period size: 52 Copynumber: 2.1 Consensus size: 51
12458468 TGACAAAGTT
* * * *
12458478 TTGACAAAAAGAATTGCTATCAATTACTGATCTACAAGTTTCATTTGAAGTT
1 TTGACAAAAAGAATTGCTATCAATTACTGATCTACAAGCTGCATGTGAAG-A
12458530 TTGACAAAAAGAATTGCTATCAATTACTGATCTACATA-CTGCAATGGTGAA-A
1 TTGACAAAAAGAATTGCTATCAATTACTGATCTACA-AGCTGC-AT-GTGAAGA
12458582 TTGAC
1 TTGAC
12458587 TTAAATTCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
52 43 0.86
53 3 0.06
54 4 0.08
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (51 bp):
TTGACAAAAAGAATTGCTATCAATTACTGATCTACAAGCTGCATGTGAAGA
Found at i:12479681 original size:19 final size:20
Alignment explanation
Indices: 12479644--12479681 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
12479634 AATTATTTAA
* *
12479644 ATTTTATTTAACATTTTTTT
1 ATTTTATTTAAAATATTTTT
12479664 ATTTT-TTTAAAATATTTT
1 ATTTTATTTAAAATATTTT
12479682 ATATATAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTATTTAAAATATTTTT
Found at i:12482847 original size:29 final size:29
Alignment explanation
Indices: 12482805--12482863 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
12482795 GATGTAGATG
12482805 TAGAAGTAGTGATATAATTAACAACTAAC
1 TAGAAGTAGTGATATAATTAACAACTAAC
12482834 TAGAAGTAGTGATATAATTAACAACTAAC
1 TAGAAGTAGTGATATAATTAACAACTAAC
12482863 T
1 T
12482864 TCAAGCTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (29 bp):
TAGAAGTAGTGATATAATTAACAACTAAC
Found at i:12484273 original size:3 final size:3
Alignment explanation
Indices: 12484265--12484290 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12484255 TGAAGGAGAG
12484265 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
12484291 GGCCTCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:12492971 original size:17 final size:16
Alignment explanation
Indices: 12492949--12492982 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12492939 GGGGATAGAG
12492949 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
12492966 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
12492982 T
1 T
12492983 AATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:12498558 original size:36 final size:36
Alignment explanation
Indices: 12498494--12498562 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
12498484 AGGCTCAAAT
*
12498494 CCTTTTACTTTATCCCATTTCCCCTCAAAGCCCAAC
1 CCTTTTACTTTATCCCATTTCACCTCAAAGCCCAAC
**
12498530 CCTTTTACTTTA-CCCTATTTCATTTCAAAGCCC
1 CCTTTTACTTTATCCC-ATTTCACCTCAAAGCCC
12498563 TGCTAGCCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 3 0.10
36 26 0.90
ACGTcount: A:0.22, C:0.38, G:0.03, T:0.38
Consensus pattern (36 bp):
CCTTTTACTTTATCCCATTTCACCTCAAAGCCCAAC
Found at i:12506817 original size:27 final size:27
Alignment explanation
Indices: 12506779--12506844 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
12506769 ACCTGGTCAT
* * *
12506779 TAAACATGGGGTCGTCCATTGGGACAG
1 TAAACATGGGGTAGCCCATTGGGACAA
*
12506806 TAAACATGGGGTAGCCCATTGGGATAA
1 TAAACATGGGGTAGCCCATTGGGACAA
*
12506833 TAAACACGGGGT
1 TAAACATGGGGT
12506845 GGAAGGGGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.21
Consensus pattern (27 bp):
TAAACATGGGGTAGCCCATTGGGACAA
Found at i:12516503 original size:15 final size:15
Alignment explanation
Indices: 12516465--12516506 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
12516455 CTATCATAAA
12516465 ATATGAATATGTGTGT
1 ATATG-ATATGTGTGT
* *
12516481 -TGTGATATGTGTTT
1 ATATGATATGTGTGT
12516495 ATATGATATGTG
1 ATATGATATGTG
12516507 ACTATTATGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (15 bp):
ATATGATATGTGTGT
Found at i:12527206 original size:13 final size:13
Alignment explanation
Indices: 12527188--12527253 Score: 55
Period size: 13 Copynumber: 5.0 Consensus size: 13
12527178 ATTAATTTAG
12527188 TAATTTTTTATTT
1 TAATTTTTTATTT
*
12527201 TAATTTTAATATTT
1 TAATTTT-TTATTT
*
12527215 T--TGTTTTTAATT
1 TAAT-TTTTTATTT
*
12527227 TAATTTTTATATTC
1 TAATTTTT-TATTT
*
12527241 TAATTGTTTATTT
1 TAATTTTTTATTT
12527254 GTTTGTTTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 6 0.15
13 18 0.44
14 17 0.41
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.70
Consensus pattern (13 bp):
TAATTTTTTATTT
Found at i:12527228 original size:20 final size:20
Alignment explanation
Indices: 12527179--12527245 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
12527169 TTTATTTCTA
*
12527179 TTAATTTAGTAATTTTTTATT
1 TTAATTTAAT-ATTTTTTATT
12527200 TTAATTTTAATATTTTTGT-TT
1 TTAA-TTTAATATTTTT-TATT
*
12527221 TTAATTTAAT-TTTTATATT
1 TTAATTTAATATTTTTTATT
*
12527240 CTAATT
1 TTAATT
12527246 GTTTATTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 1 0.03
19 11 0.28
20 6 0.15
21 16 0.40
22 6 0.15
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.67
Consensus pattern (20 bp):
TTAATTTAATATTTTTTATT
Found at i:12527253 original size:26 final size:25
Alignment explanation
Indices: 12527192--12527253 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
12527182 ATTTAGTAAT
* **
12527192 TTTTTATTTTAATTTTAATATTTTTG
1 TTTTTA-TTTAATTTTAATATTCTAA
*
12527218 TTTTTAATTTAATTTTTATATTCTAA
1 TTTTT-ATTTAATTTTAATATTCTAA
12527244 TTGTTTATTT
1 TT-TTTATTT
12527254 GTTTGTTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (25 bp):
TTTTTATTTAATTTTAATATTCTAA
Found at i:12529199 original size:35 final size:35
Alignment explanation
Indices: 12529153--12529225 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
12529143 TATGCCTTAT
12529153 ATGATGTTTAAACAACTTGGTCTTCGGGAACCCAA
1 ATGATGTTTAAACAACTTGGTCTTCGGGAACCCAA
12529188 ATGATGTTTAAACAACTTGGTCTTCGGGAACCCAA
1 ATGATGTTTAAACAACTTGGTCTTCGGGAACCCAA
12529223 ATG
1 ATG
12529226 CACTAGGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (35 bp):
ATGATGTTTAAACAACTTGGTCTTCGGGAACCCAA
Found at i:12533520 original size:44 final size:46
Alignment explanation
Indices: 12533464--12533556 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 46
12533454 TACAATATCT
* * *
12533464 ATTCTATTCAACCAAAGAAAAGAA-TGCT-ATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACTGATTACAGCTCTATTCC
**
12533508 ATTCCATTCAACCAAACAATTGAATTACTGATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACTGATTACAGCTCTATTCC
12533554 ATT
1 ATT
12533557 ACAGCTCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 20 0.48
45 3 0.07
46 19 0.45
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACTGATTACAGCTCTATTCC
Found at i:12533559 original size:16 final size:16
Alignment explanation
Indices: 12533538--12533592 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
12533528 TGAATTACTG
12533538 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
12533554 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
12533570 ATTACA-TTCCTATTCC
1 ATTACAGCT-CTATTCC
12533586 ATTACAG
1 ATTACAG
12533593 TGAACCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 1 0.03
16 33 0.97
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:12533927 original size:12 final size:12
Alignment explanation
Indices: 12533912--12533944 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
12533902 ATAGAAAATT
12533912 AAAAAAATTTG-
1 AAAAAAATTTGA
*
12533923 GAAAAAATTTGA
1 AAAAAAATTTGA
12533935 AAAAAAATTT
1 AAAAAAATTT
12533945 ATTACGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:12533991 original size:17 final size:16
Alignment explanation
Indices: 12533966--12534036 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 16
12533956 TTTTATTACT
12533966 ATAAAAAAATTTAAAAA
1 ATAAAAAAA-TTAAAAA
*
12533983 ATAATAAAATT--AAA
1 ATAAAAAAATTAAAAA
*
12533997 AT--TAAAATTAAAAA
1 ATAAAAAAATTAAAAA
*
12534011 ATAAAAAAAATAATAAA
1 ATAAAAAAATTAA-AAA
*
12534028 AGAAAAAAA
1 ATAAAAAAA
12534037 GTGAAGAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
12 7 0.16
14 10 0.22
16 9 0.20
17 19 0.42
ACGTcount: A:0.77, C:0.00, G:0.01, T:0.21
Consensus pattern (16 bp):
ATAAAAAAATTAAAAA
Found at i:12534025 original size:12 final size:13
Alignment explanation
Indices: 12533980--12534033 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 13
12533970 AAAAATTTAA
12533980 AAAATAATAAAATT
1 AAAATAATAAAA-T
12533994 AAAAT--TAAAATT
1 AAAATAATAAAA-T
12534006 AAAA-AATAAAA-
1 AAAATAATAAAAT
*
12534017 AAAATAATAAAAG
1 AAAATAATAAAAT
12534030 AAAA
1 AAAA
12534034 AAAGTGAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.11
12 18 0.50
13 9 0.25
14 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:12534502 original size:6 final size:6
Alignment explanation
Indices: 12534493--12534522 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
12534483 TATTTATTTA
12534493 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT
12534523 GCTTTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTGTT
Found at i:12534566 original size:5 final size:5
Alignment explanation
Indices: 12534543--12534576 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
12534533 TTTACTTTTA
12534543 TATTT TATGTT TA-TT TATTT TATTT TATTT TATT
1 TATTT TAT-TT TATTT TATTT TATTT TATTT TATT
12534577 ATGCATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:12546255 original size:43 final size:43
Alignment explanation
Indices: 12546098--12546256 Score: 123
Period size: 43 Copynumber: 3.7 Consensus size: 43
12546088 AATGTGACAT
* *
12546098 CGTGTAAGACCACGTCTGGGACGTTGGCCTCG--ATTTGAGATTTA
1 CGTGTAAGACCACGTCTGGGAAGTTGGCATCGTTATTT--GA-TTA
* * * *
12546142 CGTGTAAGACCATGTTTGGGAAATTGGCAT--TATATATGATTA
1 CGTGTAAGACCACGTCTGGGAAGTTGGCATCGT-TATTTGATTA
* *
12546184 TGTGTAAGACC-CTGTCTAGGACAG-TGGCATCGTTATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGA-AGTTGGCATCGTTATTTGATTA
* * *
12546227 CATGTAAGACCACGTTTGGGATGTTGGCAT
1 CGTGTAAGACCACGTCTGGGAAGTTGGCAT
12546257 TGTACGAGCT
Statistics
Matches: 89, Mismatches: 17, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
42 26 0.29
43 33 0.37
44 27 0.30
45 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGAAGTTGGCATCGTTATTTGATTA
Found at i:12564614 original size:20 final size:20
Alignment explanation
Indices: 12564589--12564633 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
12564579 TATTTTCCTG
12564589 AAAATAAAAAATCATCCAAA
1 AAAATAAAAAATCATCCAAA
* *
12564609 AAAATAAGATATCATCCAAA
1 AAAATAAAAAATCATCCAAA
12564629 AAAAT
1 AAAAT
12564634 CCCTAAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAATAAAAAATCATCCAAA
Found at i:12565021 original size:19 final size:19
Alignment explanation
Indices: 12564997--12565034 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12564987 AAGTTAATAA
*
12564997 CAAATTTGATTACAGTGGG
1 CAAATTTAATTACAGTGGG
*
12565016 CAAATTTAATTACGGTGGG
1 CAAATTTAATTACAGTGGG
12565035 TGACAGTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
CAAATTTAATTACAGTGGG
Found at i:12580833 original size:43 final size:42
Alignment explanation
Indices: 12580770--12580877 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 42
12580760 TCGTTGAATA
* * * *
12580770 ACTGAAGGAAAGATATTGGCACACATAGCGCATCATCAGACAAG
1 ACTGAAGAAAATATACTGGCACACATAACGCATCATC-GA-AAG
* * * *
12580814 -CTGAAGAAATTATACTGGCACGCATAATGCATCATCGAATG
1 ACTGAAGAAAATATACTGGCACACATAACGCATCATCGAAAG
12580855 TACTGAAGAAAATATACTGGCAC
1 -ACTGAAGAAAATATACTGGCAC
12580878 TTAAGTGCAT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
41 2 0.04
42 2 0.04
43 49 0.92
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (42 bp):
ACTGAAGAAAATATACTGGCACACATAACGCATCATCGAAAG
Found at i:12583810 original size:21 final size:19
Alignment explanation
Indices: 12583776--12583814 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
12583766 ATTAATATTA
12583776 ATATTAAATAAATATAATT
1 ATATTAAATAAATATAATT
12583795 ATATTAATATTAAATATAAT
1 ATATTAA-A-TAAATATAAT
12583815 AAAAATCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTAAATAAATATAATT
Found at i:12590176 original size:11 final size:11
Alignment explanation
Indices: 12590160--12590186 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12590150 TCACGGAATG
12590160 ATTTCGTGAAA
1 ATTTCGTGAAA
12590171 ATTTCGTGAAA
1 ATTTCGTGAAA
12590182 ATTTC
1 ATTTC
12590187 ATTCAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (11 bp):
ATTTCGTGAAA
Found at i:12592891 original size:50 final size:50
Alignment explanation
Indices: 12592817--12593159 Score: 398
Period size: 50 Copynumber: 6.8 Consensus size: 50
12592807 TCCTTTACTA
* * * ** *
12592817 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * ** *
12592867 CCCATGCCATGTCCCGGACATGGTCTTACGGGGGACCTCTCATCTTGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
12592917 CCAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTTGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* ** * *
12592967 CCAACACCATGTCCCAGACATGGTCTTACGGGGGACCACTTATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
12593017 CCAACGTCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * *
12593067 CGAACGCCACGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCATGATG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTC--GGTG
*** *
12593120 CCAATTTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
12593160 TTACCCAAAT
Statistics
Matches: 248, Mismatches: 42, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
50 209 0.84
51 2 0.01
53 37 0.15
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Done.