Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_75 ID=scaffold_75-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: 19203
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.28
Warning! 2639 characters in sequence are not A, C, G, or T
Found at i:3672 original size:10 final size:10
Alignment explanation
Indices: 3657--3720 Score: 64
Period size: 10 Copynumber: 6.5 Consensus size: 10
3647 TCAGTGGGGG
3657 AAAAAAGCAA
1 AAAAAAGCAA
3667 AAAAAAGCAA
1 AAAAAAGCAA
*
3677 AAAAAACGAGAA
1 AAAAAA-G-CAA
3689 AACAAAAGC-A
1 AA-AAAAGCAA
3699 AAAAAA-C-A
1 AAAAAAGCAA
3707 AAAAAA-CAA
1 AAAAAAGCAA
3716 AAAAA
1 AAAAA
3721 TAAAAAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
8 9 0.19
9 10 0.21
10 19 0.40
11 1 0.02
12 5 0.10
13 4 0.08
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGCAA
Found at i:3705 original size:22 final size:23
Alignment explanation
Indices: 3665--3717 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
3655 GGAAAAAAGC
* *
3665 AAAA-AAAAGCAAAAAAAACGAG
1 AAAACAAAAGCAAAAAAAACAAA
3687 AAAACAAAAGC-AAAAAAACAAA
1 AAAACAAAAGCAAAAAAAACAAA
3709 AAAACAAAA
1 AAAACAAAA
3718 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (23 bp):
AAAACAAAAGCAAAAAAAACAAA
Found at i:3725 original size:22 final size:22
Alignment explanation
Indices: 3665--3727 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
3655 GGAAAAAAGC
* *
3665 AAAA-AAAAGCAAAAAAAACGAG
1 AAAACAAAAG-AAAAAAAACAAA
*
3687 AAAACAAAAGCAAAAAAACAAA
1 AAAACAAAAGAAAAAAAACAAA
*
3709 AAAACAAAAAAATAAAAAA
1 AAAACAAAAGAA-AAAAAA
3728 ATAAGAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.83, C:0.10, G:0.06, T:0.02
Consensus pattern (22 bp):
AAAACAAAAGAAAAAAAACAAA
Found at i:3731 original size:8 final size:8
Alignment explanation
Indices: 3666--3728 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
3656 GAAAAAAGCA
3666 AAAAAAAGC
1 AAAAAAA-C
3675 AAAAAAAAC
1 -AAAAAAAC
* *
3684 GAGAAAAC
1 AAAAAAAC
*
3692 --AAAAGC
1 AAAAAAAC
3698 AAAAAAAC
1 AAAAAAAC
3706 AAAAAAAC
1 AAAAAAAC
*
3714 AAAAAAAT
1 AAAAAAAC
3722 AAAAAAA
1 AAAAAAA
3729 TAAGAGAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
6 4 0.09
8 33 0.73
9 1 0.02
10 7 0.16
ACGTcount: A:0.83, C:0.10, G:0.06, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:4195 original size:18 final size:18
Alignment explanation
Indices: 4155--4202 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
4145 ACTTTACTTT
*
4155 AAAAAAAGAAACGAAAAG
1 AAAAAAAGAAAAGAAAAG
*
4173 AAAAAAAGAAAAGAATA-
1 AAAAAAAGAAAAGAAAAG
*
4190 ACAAAAAGAAAAG
1 AAAAAAAGAAAAG
4203 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAAAGAAAAG
Found at i:5412 original size:88 final size:87
Alignment explanation
Indices: 5199--5519 Score: 401
Period size: 88 Copynumber: 3.7 Consensus size: 87
5189 GGTTGCAATG
* *
5199 GAGCTGGTCAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAAACAAAG
1 GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAA-
* * **
5263 CCTTTCCTCTATCGGTTGCAGTG
65 CCTTGCCTCTATCGGTTGTAGCA
* * *
5286 GAGTTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAACACACAAA
1 GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-ACACAAA
* *
5351 CCTTGCATCTTTCGGTTGTAGCA
65 CCTTGCCTCTATCGGTTGTAGCA
* *
5374 GAGCTGGTTGAAGATAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAA
1 GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-ACACAAA
* *
5439 CCTTGCCTCTCTCGTTTGTAGCA
65 CCTTGCCTCTATCGGTTGTAGCA
* * * * ** *
5462 GAACTGGTTAAAGATTGCAGATCATGCCTTCCTGTATTTGGCAGCGACGCAGATCGAA
1 GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCA-TTAACAGCGAAGCAGATCGAA
5520 GATGGCAGAT
Statistics
Matches: 204, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
87 50 0.25
88 130 0.64
89 24 0.12
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (87 bp):
GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAC
CTTGCCTCTATCGGTTGTAGCA
Found at i:5745 original size:134 final size:134
Alignment explanation
Indices: 5472--6255 Score: 1370
Period size: 134 Copynumber: 5.8 Consensus size: 134
5462 GAACTGGTTA
* *
5472 AAGATTGCAGATCATGCCTTCCTGTATTTGGCAGCGACGCAGATCGAAGATGGCAGATTTTACCT
1 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
* * *
5537 CCCTGTGACTACAGACGAGTACATTGAAGCCGATAACTCTATCTTCCTGTATTTGGCAGTGGAAT
66 CCC--TGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTATATTTGGCAGTGGAAT
5602 AGATTG
129 AGATTG
*
5608 AAGATTGCATATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
1 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
5673 CCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTATATTTGGCAGTGGAATAG
66 CCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTATATTTGGCAGTGGAATAG
5738 ATTG
131 ATTG
5742 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
1 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
*
5807 CCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAG
66 CCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTATATTTGGCAGTGGAATAG
5872 ATTG
131 ATTG
*
5876 AAGATTGCATATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
1 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
5941 CCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTATATTTGGCAGTGGAATAG
66 CCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTATATTTGGCAGTGGAATAG
6006 ATTG
131 ATTG
6010 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
1 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
*
6075 CCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAG
66 CCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTATATTTGGCAGTGGAATAG
6140 ATTG
131 ATTG
* * * *
6144 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGTAGGTCAAAGATGGCGGATTTTACCT
1 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
* * * * * **
6209 CCCCGATTACGGTGGAGTACATTGAAGCCAATAGTTCTATCTCCCTA
66 CCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTA
6256 AGCAGTAGCG
Statistics
Matches: 624, Mismatches: 24, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
134 559 0.90
136 65 0.10
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (134 bp):
AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
CCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTATATTTGGCAGTGGAATAG
ATTG
Found at i:6810 original size:84 final size:82
Alignment explanation
Indices: 6246--7099 Score: 1237
Period size: 82 Copynumber: 10.3 Consensus size: 82
6236 CCAATAGTTC
*
6246 TATCTCCCTAAGCAGTAGCGGAGCGGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
1 TATCTCCCTAAGCAGTAGCGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
6311 CAGATCGCATCAAGTCT
66 CAGATCGCATCAAGTCT
*
6328 TATCTCCCTAAGCAGTAGCGGAGCGGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
1 TATCTCCCTAAGCAGTAGCGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
6393 CAGATCGCATCAAGTCT
66 CAGATCGCATCAAGTCT
* * *
6410 TATCTCCCTAAGCAGTAGCGGAGCGGACAAAACCACAGATCTTATCTTCCTAAGCAATAGTGAAG
1 TATCTCCCTAAGCAGTAGCGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
6475 CAGATCGCATCAAGTCT
66 CAGATCGCATCAAGTCT
*
6492 TATCTCCCTAAGCAGTAGCGGAGCGGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
1 TATCTCCCTAAGCAGTAGCGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
6557 CAGATCGCATCAAGTCT
66 CAGATCGCATCAAGTCT
* * *
6574 TATCTCCCTAAGCAGTAGCGGAGCGGACAAAACCATAGATCTGATCTCCCTAAGCAATAGTGGAG
1 TATCTCCCTAAGCAGTAGCGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
*
6639 CAGATCACATCAAGTCT
66 CAGATCGCATCAAGTCT
6656 TATCTCCCTAAGCAGTAGCGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
1 TATCTCCCTAAGCAGTAGCGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
6721 CAGATCGCATCAAGTCT
66 CAGATCGCATCAAGTCT
* * * * ** * *
6738 TATCTTCCTAAGTAATAGTGGAGCAGACAAAAGAAACCAGATTTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGCGGAGCAGACAAAA-CCA-CAGATCTTATCTCCCTAAGCAATAGTGG
* *
6803 AGCAGATCACATCAACTCT
64 AGCAGATCGCATCAAGTCT
* * * * *
6822 TATCTACCTAAACAGTAGTGGAGCAGACGAAAGA-AACCAGATCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTAAGCAGTAGCGGAGCAGAC-AAA-ACCA-CAGATCTTATCTCCCTAAGCAATAGTG
*
6886 GAGCAGATCACATCAAGTCT
63 GAGCAGATCGCATCAAGTCT
* * *
6906 TATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGA-AACCAGATCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTAAGCAGTAGCGGAGCAGAC-AAA-ACCA-CAGATCTTATCTCCCTAAGCAATAGTG
* *
6970 GAGCAAATCACATCAAGTCT
63 GAGCAGATCGCATCAAGTCT
* * * * * *
6990 TATCTCCCTAAGAAATAGTGGAGCAGACGAAAGA-AACTAGATCTTATCTCCCTAAGCAGTGGTG
1 TATCTCCCTAAGCAGTAGCGGAGCAGAC-AAA-ACCAC-AGATCTTATCTCCCTAAGCAATAGTG
7054 GAGCAGATCGCATCAAGTCT
63 GAGCAGATCGCATCAAGTCT
* *
7074 TATCTCCCTAAACAGTAGTGGAGCAG
1 TATCTCCCTAAGCAGTAGCGGAGCAG
7100 GTTGAAGATA
Statistics
Matches: 729, Mismatches: 38, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
82 427 0.59
83 2 0.00
84 296 0.41
85 3 0.00
86 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (82 bp):
TATCTCCCTAAGCAGTAGCGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAG
CAGATCGCATCAAGTCT
Found at i:16782 original size:108 final size:108
Alignment explanation
Indices: 16593--16788 Score: 279
Period size: 108 Copynumber: 1.8 Consensus size: 108
16583 TTTGTATTCT
** * *
16593 AGCAAAATTTGCTATCTTGATTGATTTGTTCATTTAGAGCTTTGCTCTTAACAAATTTCCATCTT
1 AGCAAAACATGCTATCTTGATTGATTTGTTCATTTAGAGCTTTACTCTCAACAAATTTCCATCTT
*
16658 ATCCGTTGTGATAATCTTTTTCATCTTATTCATCTCGTATCTC
66 ATCCCTTGTGATAATCTTTTTCATCTTATTCATCTCGTATCTC
** *
16701 AGCAAAACATGCTATCTTGATTGATTTGTTTGTTTAGAGCTTTACTCTCAACAAAATTT-CATTT
1 AGCAAAACATGCTATCTTGATTGATTTGTTCATTTAGAGCTTTACTCTCAAC-AAATTTCCATCT
*
16765 TGTCCACTT-TGATAATCTTTTTCA
65 TATCC-CTTGTGATAATCTTTTTCA
16789 AGCATTTTTC
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
108 69 0.90
109 8 0.10
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (108 bp):
AGCAAAACATGCTATCTTGATTGATTTGTTCATTTAGAGCTTTACTCTCAACAAATTTCCATCTT
ATCCCTTGTGATAATCTTTTTCATCTTATTCATCTCGTATCTC
Found at i:17366 original size:46 final size:46
Alignment explanation
Indices: 17311--18183 Score: 231
Period size: 46 Copynumber: 19.4 Consensus size: 46
17301 ATAACTCTAT
*
17311 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTACAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGACAGATCTTGC
* * * * * * *
17357 CTTCCTGTATTTGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGACAGATCTTGC
* * * * * * ** *
17403 CTCCCTG-A-CT-ACAGAGGAGTACATTAAAGCCGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGACAGA-TCT-TGC
*
17445 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTG-CAGATCTTGT
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGA-TGACAGATCTTGC
* * * * * * *
17491 CTTCCTGTATTTGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGACAGATCTTGC
* * * * * ** *
17537 CTCCCTG-A-CT-ACAGAGGAGTACATTGAAGCCGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGACAGA-TCT-TGC
17579 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTG-CAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGA-TGACAGATCTTGC
* * * * * *
17625 CTTCCTGTATTTGGCAG-CGAAGCAGATCGAAGATGACAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGACAGATCTTGC
* * * * * ** *
17671 CTCCCTG-A-CT-ACAGAGGAGTACATTGAAGCCGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGACAGA-TCT-TGC
17713 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTG-CAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGA-TGACAGATCTTGC
* * * * * * * *
17759 CTTCCTGTATTTGGCAG-CGAAGCAGATCGTAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGACAGATCTTGC
* * * * * * * * *
17805 TTTCCTG-A-CT-ACAGAGGAGTACATTGAAGCTGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGACAGA-TCT-TGC
17847 CT-CCTGTATTTGGCAGTGGAATAGATTGAAAGATTG-CAGATCTTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTG-AAGA-TGACAGATC-TTGC
* * * * * * * * *
17894 CTTTCCTGTAATTTGGCAGCGAAAGCAGATCGTAGATGGCAGATAATTAC
1 C-TCCCTGT-ATTTGGCAGTGGAA-TAGATTGAAGATGACAGAT-CTTGC
* * * * * * * ** *
17944 TTTCCTG-A-CT-ACAGAGGAGTACATTGAAGCCGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGACAGA-TCT-TGC
*
17986 CTCCCTGTATTTGGTAGTGGAATAGATTGAAGATTG-CAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGA-TGACAGATCTTGC
* * * * * *
18032 CTTCCTGTATTTGGCAG-CGAAGCAGAATCGAAGATGACAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAG-ATTGAAGATGACAGATCTTGC
* * * * * * ** *
18079 CTCCCTG-A-CT-ACAGAGGAGTACATTAAAGCCGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGACAGA-TCT-TGC
*
18121 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTG-CAGATCTTGT
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGA-TGACAGATCTTGC
*
18167 CTTCCTGTATTTGGCAG
1 CTCCCTGTATTTGGCAG
18184 CGAAGCAGGT
Statistics
Matches: 574, Mismatches: 176, Indels: 154
0.63 0.19 0.17
Matches are distributed among these distances:
41 4 0.01
42 40 0.07
43 74 0.13
44 53 0.09
45 132 0.23
46 206 0.36
47 23 0.04
48 1 0.00
49 13 0.02
50 23 0.04
51 5 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (46 bp):
CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGACAGATCTTGC
Found at i:17444 original size:134 final size:134
Alignment explanation
Indices: 17213--18261 Score: 1769
Period size: 134 Copynumber: 7.8 Consensus size: 134
17203 ATGAAGTTAA
*
17213 CAGATCTTGCCTTCCTGTATTTGGTAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
1 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
*
17278 TACAGAGGAGTATATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
66 TACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
*
17343 ATTA
131 ATTG
17347 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
1 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
*
17412 TACAGAGGAGTACATTAAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
66 TACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
17477 ATTG
131 ATTG
*
17481 CAGATCTTGTCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
1 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
17546 TACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
66 TACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
17611 ATTG
131 ATTG
*
17615 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGACAGATTTTACCTCCCTGAC
1 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
17680 TACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
66 TACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
17745 ATTG
131 ATTG
* * *
17749 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGTAGATGGCAGATTTTACTTTCCTGAC
1 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
*
17814 TACAGAGGAGTACATTGAAGCTGATAACTCTATCT-CCTGTATTTGGCAGTGGAATAGATTGAAA
66 TACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTG-AA
17878 GATTG
130 GATTG
* * * *
17883 CAGATCTTTGCCTTTCCTGTAATTTGGCAGCGAAAGCAGATCGTAGATGGCAGATAATTACTTTC
1 CAGATC-TTGCC-TTCCTGT-ATTTGGCAGCG-AAGCAGATCGAAGATGGCAGAT-TTTACCTCC
*
17948 CTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGTAGTGGAATAGAT
61 CTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGAT
18013 TGAAGATTG
126 TGAAGATTG
*
18022 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGAATCGAAGATGACAGATTTTACCTCCCTGA
1 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAG-ATCGAAGATGGCAGATTTTACCTCCCTGA
*
18087 CTACAGAGGAGTACATTAAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAA
65 CTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAA
18152 GATTG
130 GATTG
* * * * *
18157 CAGATCTTGTCTTCCTGTATTTGGCAGCGAAGCAGGTCGAAGATGGCGGATTTTACCTCCCCGAT
1 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
* * * **
18222 TACGGTGGAGTACATTAAAGCC-AGTAGTTCTATCTCCCTG
66 TACAGAGGAGTACATTGAAGCCGA-TAACTCTATCTCCCTG
18262 GGCAACAGTG
Statistics
Matches: 873, Mismatches: 33, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
133 27 0.03
134 561 0.64
135 123 0.14
136 32 0.04
137 18 0.02
138 27 0.03
139 60 0.07
140 25 0.03
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (134 bp):
CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
TACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
ATTG
Found at i:18379 original size:82 final size:82
Alignment explanation
Indices: 18288--18507 Score: 388
Period size: 81 Copynumber: 2.7 Consensus size: 82
18278 AGTGAAGATT
18288 ACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
1 ACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
*
18353 GCGGAGCAGACAGAACC
66 GCGGAGCAGACAAAACC
18370 ACAGATCTTATCTCCCTAAGCAA-AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
1 ACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
*
18434 GCGGAGCGGACAAAACC
66 GCGGAGCAGACAAAACC
* * *
18451 ACAGACCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAATCTTATCTCCCT
1 ACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCT
18508 GAAGTTGCAG
Statistics
Matches: 132, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
81 77 0.58
82 55 0.42
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (82 bp):
ACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
GCGGAGCAGACAAAACC
Found at i:18389 original size:42 final size:42
Alignment explanation
Indices: 18288--18507 Score: 242
Period size: 40 Copynumber: 5.4 Consensus size: 42
18278 AGTGAAGATT
* * *
18288 ACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATC
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAACC
*
18330 A-AG-TCTTATCTCCCTAAGCAGTAGCGGAGCAGA-CAGAACC
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAACC
* * *
18370 ACAGATCTTATCTCCCTAAGCA-AAGTGGAGCAGATCGCATC
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAACC
* * *
18411 A-AG-TCTTATCTCCCTAAGCAGTAGCGGAGCGGA-CAAAACC
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAACC
* * *
18451 ACAGACCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATC
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAACC
18493 A-A-ATCTTATCTCCCT
1 ACAGATCTTATCTCCCT
18508 GAAGTTGCAG
Statistics
Matches: 148, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
39 19 0.13
40 58 0.39
41 21 0.14
42 49 0.33
43 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (42 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAACC
Done.