Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 188 of 205
Found at i:55863896 original size:38 final size:38
Alignment explanation
Indices: 55863844--55863919 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
55863834 ATTAGAGTCC
*
55863844 ATTCAAATCGAGTGAGTTTAGCATACTTAACAAAATTT
1 ATTCAAATCAAGTGAGTTTAGCATACTTAACAAAATTT
55863882 ATTCAAATCAAGTGAGTTTAGCATACTTAACAAAATTT
1 ATTCAAATCAAGTGAGTTTAGCATACTTAACAAAATTT
55863920 CATACTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (38 bp):
ATTCAAATCAAGTGAGTTTAGCATACTTAACAAAATTT
Found at i:55864699 original size:3 final size:3
Alignment explanation
Indices: 55864691--55864718 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55864681 CTCAGTGGGA
55864691 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
55864719 TTTCAGGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:55869424 original size:30 final size:30
Alignment explanation
Indices: 55869367--55869424 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
55869357 TGCCTTTGAA
* *
55869367 AATATTTACAAAAAGAGACATCTAATTTCT
1 AATATTTACAAAAAGAGACACCAAATTTCT
55869397 AATATTTACAAAAAGAG-CAACCAAATTT
1 AATATTTACAAAAAGAGAC-ACCAAATTT
55869425 TGAAAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACACCAAATTTCT
Found at i:55872141 original size:33 final size:33
Alignment explanation
Indices: 55872104--55872182 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
55872094 CCAGGATTCG
*
55872104 GTTTCTTGATTTTCTTGAAAATAAGAAAGTGAA
1 GTTTCTTGATTTTCTTGAAAACAAGAAAGTGAA
55872137 GTTTCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 GTTTCTTGATTTTCTTGAAAACAAGAAAGTGAA
55872170 ---TCTTGATTTTCTT
1 GTTTCTTGATTTTCTT
55872183 CTAAGGCCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
30 13 0.29
33 32 0.71
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (33 bp):
GTTTCTTGATTTTCTTGAAAACAAGAAAGTGAA
Found at i:55872877 original size:235 final size:234
Alignment explanation
Indices: 55872465--55872935 Score: 897
Period size: 235 Copynumber: 2.0 Consensus size: 234
55872455 TTGATCCGCT
55872465 TGAGTACTTGGAAAGGCCCATCGCCCCTTGGGTCCAACTTGGTCTTTCTTTTTGTAGGAAATCGT
1 TGAGTACTTGGAAAGGCCCATCGCCCCTTGGGTCCAACTTGGTCTTTCTTTTTGTAGGAAATCGT
* *
55872530 TCTTTCCTCAAATGGACCCAAACCCAATCTCCGGGTTCTAGTACAACCCGTTTGCGCCCCTTGTT
66 TCTTTCCTCAAATGGACCCAAACCCAATCTCCGGGTTCTAGAACAACCCGTTTACGCCCCTTGTT
55872595 TGCTTTGTTGGTGTTGGCATCATTTTTTTTGGCTATTCGTTGCCTAGCCTTCTCATGTAAGGATT
131 TGCTTTGTTGGTGTTGGCATCATTTTTTTTGGCTATTCGTTGCCTAGCCTTCTCATGTAAGGATT
55872660 TCACGAACTCAGCTTTCTGTTCGCCATCTAAATTAATAA
196 TCACGAACTCAGCTTTCTGTTCGCCATCTAAATTAATAA
55872699 TNGAGTACTTGGAAAGGCCCATCGCCCCTTGGGTCCAACTTGGTCTTTCTTTTTGTAGGAAATCG
1 T-GAGTACTTGGAAAGGCCCATCGCCCCTTGGGTCCAACTTGGTCTTTCTTTTTGTAGGAAATCG
* *
55872764 TTCTTTCCTCAAATGGACCCAAACCCAATCTCTGGGTTCTAGAACAACCCGTTTATGCCCCTTGT
65 TTCTTTCCTCAAATGGACCCAAACCCAATCTCCGGGTTCTAGAACAACCCGTTTACGCCCCTTGT
55872829 TTGCTTTGTTGGTGTTGGCATCATTTTTTTTGGCTATTCGTTGCCTAGCCTTCTCATGTAAGGAT
130 TTGCTTTGTTGGTGTTGGCATCATTTTTTTTGGCTATTCGTTGCCTAGCCTTCTCATGTAAGGAT
55872894 TTCACGAACTCAGCTTTCTGTTCGCCATCTAAATTAATAA
195 TTCACGAACTCAGCTTTCTGTTCGCCATCTAAATTAATAA
55872934 TG
1 TG
55872936 TGTTGAAGAG
Statistics
Matches: 232, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
234 2 0.01
235 230 0.99
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (234 bp):
TGAGTACTTGGAAAGGCCCATCGCCCCTTGGGTCCAACTTGGTCTTTCTTTTTGTAGGAAATCGT
TCTTTCCTCAAATGGACCCAAACCCAATCTCCGGGTTCTAGAACAACCCGTTTACGCCCCTTGTT
TGCTTTGTTGGTGTTGGCATCATTTTTTTTGGCTATTCGTTGCCTAGCCTTCTCATGTAAGGATT
TCACGAACTCAGCTTTCTGTTCGCCATCTAAATTAATAA
Found at i:55879373 original size:40 final size:40
Alignment explanation
Indices: 55879275--55879577 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
55879265 TCCTCGTTCA
* * * * *
55879275 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
55879314 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
55879354 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
55879394 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
55879434 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
55879474 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
55879514 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
55879554 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
55879578 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 38 0.16
40 194 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:55893648 original size:20 final size:18
Alignment explanation
Indices: 55893623--55893659 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
55893613 TATTGTGGCA
55893623 AAAAGAAAGAGAAAAAAGAG
1 AAAAGAAA-A-AAAAAAGAG
55893643 AAAAGAAAAAAAAAAGA
1 AAAAGAAAAAAAAAAGA
55893660 ATGAGATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAGAG
Found at i:55893653 original size:16 final size:16
Alignment explanation
Indices: 55893622--55893660 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
55893612 ATATTGTGGC
*
55893622 AAAAAG-AAAGAGAAA
1 AAAAAGAAAAGAAAAA
*
55893637 AAAGAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
55893653 AAAAAGAA
1 AAAAAGAA
55893661 TGAGATGGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:55904985 original size:16 final size:16
Alignment explanation
Indices: 55904964--55904995 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55904954 GTCCACATAC
55904964 ATCAGTATGCATTAGG
1 ATCAGTATGCATTAGG
*
55904980 ATCAGTATGTATTAGG
1 ATCAGTATGCATTAGG
55904996 CCCAATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.34
Consensus pattern (16 bp):
ATCAGTATGCATTAGG
Found at i:55918465 original size:50 final size:50
Alignment explanation
Indices: 55918266--55918653 Score: 395
Period size: 50 Copynumber: 7.6 Consensus size: 50
55918256 CGATCTCGTA
* * * * *
55918266 TAAGACCATGTCTGGAACATGGCATCGACATCGATATGTGA-G--CCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGGTCCCA-TG
**
55918314 TAAGACCATGTCTGGGACATGGCATTGGCATTACTAAAATTATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGC---AC--CGA-TATGAGAGGTCCCATG
* **
55918370 TAAGACCATGTATGGGACATGGCATTGGCATTACTAAAATTATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGC---AC--CGA-TATGAGAGGTCCCATG
*
55918426 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGGTCCCATG
* *
55918476 TAAGACCATGTATGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGGTCCCATG
* * * **
55918526 TAAGACCATGTCTGGGGCATGGCGTTGGCACCGAGATGAGAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGGTCCCATG
* * ** *
55918576 TAAGACCATGTATGGGACATGGCATGGGCACCGATATGAGAACTCTCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGGTCCCATG
* * * *
55918626 TAAGACCGTATCTAGGATATGGCATTGG
1 TAAGACCATGTCTGGGACATGGCATTGG
55918654 TAGTACAGGA
Statistics
Matches: 297, Mismatches: 34, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
48 26 0.09
50 171 0.58
51 2 0.01
53 3 0.01
54 6 0.02
55 1 0.00
56 85 0.29
57 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGGTCCCATG
Found at i:55919694 original size:64 final size:64
Alignment explanation
Indices: 55919591--55919720 Score: 217
Period size: 64 Copynumber: 2.0 Consensus size: 64
55919581 AACTATTAGG
* * *
55919591 ATATTAAGGGAGTTTAGCGTGCTCTCTGATTATTTGCACATC-GATGCTCTTTGATTATTAGCAC
1 ATATTAACGGAGTTTAGCGTGCTCTCTAATTATTAGCACATCAG-TGCTCTTTGATTATTAGCAC
55919655 ATATTAACGGAGTTTAGCGTGCTCTCTAATTATTAGCACATCAGTGCTCTTTGATTATTAGCAC
1 ATATTAACGGAGTTTAGCGTGCTCTCTAATTATTAGCACATCAGTGCTCTTTGATTATTAGCAC
55919719 AT
1 AT
55919721 TTATGTTCTT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 61 0.98
65 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (64 bp):
ATATTAACGGAGTTTAGCGTGCTCTCTAATTATTAGCACATCAGTGCTCTTTGATTATTAGCAC
Found at i:55919732 original size:25 final size:25
Alignment explanation
Indices: 55919673--55919720 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
55919663 GGAGTTTAGC
* *
55919673 GTGCTCTCTAATTATTAGCACATCA
1 GTGCTCTTTGATTATTAGCACATCA
55919698 GTGCTCTTTGATTATTAGCACAT
1 GTGCTCTTTGATTATTAGCACAT
55919721 TTATGTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (25 bp):
GTGCTCTTTGATTATTAGCACATCA
Found at i:55922749 original size:27 final size:27
Alignment explanation
Indices: 55922717--55923104 Score: 418
Period size: 27 Copynumber: 14.4 Consensus size: 27
55922707 ATTTTGGTAA
*
55922717 TTGGTAATTTTACCCTTCGAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
*
55922744 TTGGTAATTTTACCCATCAAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
* **
55922771 TCT-ATAATTTTACCCATTAAGGGTATT
1 T-TGGTAATTTTACCCATCGAGGGTATT
*
55922798 TTAGTAATTTTACCCATCGAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
* *
55922825 TTGATAATTTTACACATCGAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
* *
55922852 TCGATAATTTTACCCATCGAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
* **
55922879 TTGGTCATTTTACCCATTAAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
* * * * *
55922906 TCGATTATTTTACCCTTTGAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
* * * *
55922933 TCGATCATTTTACCCATCGAGAGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
**
55922960 TCAGTAATTTTACCCATCGAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
* * * *
55922987 TCGGTAGTTTTAACTATCGAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
* * * * *
55923014 TCGGCAGTTTTACCCATCAAAGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
* *
55923041 TTAGTAATTTTTCCCATCGAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
* *
55923068 TTGGTAACTTTACCCATTGAGGGTATT
1 TTGGTAATTTTACCCATCGAGGGTATT
*
55923095 TCGGTAATTT
1 TTGGTAATTT
55923105 AGGGCCATTA
Statistics
Matches: 307, Mismatches: 52, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
26 1 0.00
27 305 0.99
28 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (27 bp):
TTGGTAATTTTACCCATCGAGGGTATT
Found at i:55922859 original size:81 final size:81
Alignment explanation
Indices: 55922720--55923104 Score: 482
Period size: 81 Copynumber: 4.8 Consensus size: 81
55922710 TTGGTAATTG
* * *
55922720 GTAATTTTACCCTTCGAGGGTATTTTGGTAATTTTACCCATCAAGGGTATTTCTATAATTTTACC
1 GTAATTTTACCCATCGAGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTCGATAATTTTACC
*
55922785 CATTAAGGGTATTTTA
66 CATCAAGGGTATTTTA
* *
55922801 GTAATTTTACCCATCGAGGGTATTTTGATAATTTTACACATCGAGGGTATTTCGATAATTTTACC
1 GTAATTTTACCCATCGAGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTCGATAATTTTACC
* *
55922866 CATCGAGGGTATTTTG
66 CATCAAGGGTATTTTA
* ** * * * * * *
55922882 GTCATTTTACCCATTAAGGGTATTTCGATTATTTTACCCTTTGAGGGTATTTCGATCATTTTACC
1 GTAATTTTACCCATCGAGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTCGATAATTTTACC
* * *
55922947 CATCGAGAGTATTTCA
66 CATCAAGGGTATTTTA
* * * * ** *
55922963 GTAATTTTACCCATCGAGGGTATTTCGGTAGTTTTAACTATCGAGGGTATTTCGGCAGTTTTACC
1 GTAATTTTACCCATCGAGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTCGATAATTTTACC
*
55923028 CATCAAAGGTATTTTA
66 CATCAAGGGTATTTTA
* * * *
55923044 GTAATTTTTCCCATCGAGGGTATTTTGGTAACTTTACCCATTGAGGGTATTTCGGTAATTT
1 GTAATTTTACCCATCGAGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTCGATAATTT
55923105 AGGGCCATTA
Statistics
Matches: 257, Mismatches: 47, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 257 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (81 bp):
GTAATTTTACCCATCGAGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTCGATAATTTTACC
CATCAAGGGTATTTTA
Found at i:55929516 original size:25 final size:25
Alignment explanation
Indices: 55929415--55929532 Score: 107
Period size: 25 Copynumber: 4.7 Consensus size: 25
55929405 GATACTCCAC
* *
55929415 AGCTCGTGTGAGCATACCGACTTAC
1 AGCTCGTGTGAGCATACAGACTTAT
55929440 AGCTCGTGTGAGCATATCA-ACTTAT
1 AGCTCGTGTGAGCATA-CAGACTTAT
* * * *
55929465 AGCTTGTGAGAGCATATCGGTC-TAT
1 AGCTCGTGTGAGCATA-CAGACTTAT
55929490 AGCTCGTGTGAGCATACAGA-TTCAT
1 AGCTCGTGTGAGCATACAGACTT-AT
* * *
55929515 AGTTCATATGAGCATACA
1 AGCTCGTGTGAGCATACA
55929533 TGTACAAGAT
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
24 3 0.04
25 71 0.93
26 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (25 bp):
AGCTCGTGTGAGCATACAGACTTAT
Found at i:55932757 original size:13 final size:13
Alignment explanation
Indices: 55932717--55932757 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
55932707 TGTAATAATT
55932717 AAAACA-AA-TTA
1 AAAACATAATTTA
*
55932728 AAAACATACATTAA
1 AAAACATA-ATTTA
55932742 AAAACATAATTTA
1 AAAACATAATTTA
55932755 AAA
1 AAA
55932758 TGTCCAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 6 0.24
12 1 0.04
13 8 0.32
14 10 0.40
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAACATAATTTA
Found at i:55932897 original size:20 final size:20
Alignment explanation
Indices: 55932868--55932941 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
55932858 AGCTAATAAC
55932868 GAGCTC-AATGAGCTTAATT
1 GAGCTCGAATGAGCTTAATT
* * *
55932887 GAGCTCGAATGCGCTGACTT
1 GAGCTCGAATGAGCTTAATT
*
55932907 GAGCTCCAATGAGC-TAACTT
1 GAGCTCGAATGAGCTTAA-TT
55932927 GAGCTCGAATGAGCT
1 GAGCTCGAATGAGCT
55932942 GAATCACATG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.16
20 37 0.84
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (20 bp):
GAGCTCGAATGAGCTTAATT
Found at i:55932918 original size:40 final size:39
Alignment explanation
Indices: 55932868--55932943 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 39
55932858 AGCTAATAAC
*
55932868 GAGCTCAATGAGCTTAA-TTGAGCTCGAATGCGCTGACTT
1 GAGCTCAATGAGC-TAACTTGAGCTCGAATGAGCTGACTT
55932907 GAGCTCCAATGAGCTAACTTGAGCTCGAATGAGCTGA
1 GAGCT-CAATGAGCTAACTTGAGCTCGAATGAGCTGA
55932944 ATCACATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
39 8 0.24
40 26 0.76
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (39 bp):
GAGCTCAATGAGCTAACTTGAGCTCGAATGAGCTGACTT
Found at i:55937198 original size:20 final size:21
Alignment explanation
Indices: 55937175--55937220 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
55937165 AGTTCAATTC
55937175 AGCTCAACT-TTAGCTCAATG
1 AGCTCAACTCTTAGCTCAATG
**
55937195 AGCTC-GTTCTTAGCTCAATG
1 AGCTCAACTCTTAGCTCAATG
55937215 AGCTCA
1 AGCTCA
55937221 TTTTTAGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (21 bp):
AGCTCAACTCTTAGCTCAATG
Found at i:55937227 original size:20 final size:20
Alignment explanation
Indices: 55937183--55937229 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
55937173 TCAGCTCAAC
*
55937183 TTTAGCTCAATGAGCTCGTT
1 TTTAGCTCAATGAGCTCATT
*
55937203 CTTAGCTCAATGAGCTCATT
1 TTTAGCTCAATGAGCTCATT
55937223 TTTAGCT
1 TTTAGCT
55937230 TACTTTAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTAGCTCAATGAGCTCATT
Found at i:55938479 original size:15 final size:16
Alignment explanation
Indices: 55938459--55938491 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
55938449 CTCCATCAAT
55938459 TACCTT-TTTCTATTC
1 TACCTTGTTTCTATTC
55938474 TACCTTGTTTCTATTC
1 TACCTTGTTTCTATTC
55938490 TA
1 TA
55938492 AACCGAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.24, G:0.03, T:0.58
Consensus pattern (16 bp):
TACCTTGTTTCTATTC
Found at i:55946407 original size:49 final size:49
Alignment explanation
Indices: 55946354--55946512 Score: 318
Period size: 49 Copynumber: 3.2 Consensus size: 49
55946344 CCATCCTGAA
55946354 TGGCCCAACAACAATGACTTTCACTATTCTTACATTTTACCATCCTAGG
1 TGGCCCAACAACAATGACTTTCACTATTCTTACATTTTACCATCCTAGG
55946403 TGGCCCAACAACAATGACTTTCACTATTCTTACATTTTACCATCCTAGG
1 TGGCCCAACAACAATGACTTTCACTATTCTTACATTTTACCATCCTAGG
55946452 TGGCCCAACAACAATGACTTTCACTATTCTTACATTTTACCATCCTAGG
1 TGGCCCAACAACAATGACTTTCACTATTCTTACATTTTACCATCCTAGG
55946501 TGGCCCAACAAC
1 TGGCCCAACAAC
55946513 GATCGGATGG
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 110 1.00
ACGTcount: A:0.29, C:0.30, G:0.11, T:0.31
Consensus pattern (49 bp):
TGGCCCAACAACAATGACTTTCACTATTCTTACATTTTACCATCCTAGG
Found at i:55954567 original size:20 final size:20
Alignment explanation
Indices: 55954542--55954580 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55954532 GCTACTCATA
55954542 TTTTCA-AAAACTTATCAGAG
1 TTTTCAGAAAACTTA-CAGAG
*
55954562 TTTTCAGAACACTTACAGA
1 TTTTCAGAAAACTTACAGA
55954581 ATTGGCGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (20 bp):
TTTTCAGAAAACTTACAGAG
Found at i:55955155 original size:16 final size:16
Alignment explanation
Indices: 55955130--55955160 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55955120 ATCGACCCGT
*
55955130 CAAGTTTGGGGATTAG
1 CAAGTCTGGGGATTAG
55955146 CAAGTCTGGGGATTA
1 CAAGTCTGGGGATTA
55955161 CCTATACAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.35, T:0.29
Consensus pattern (16 bp):
CAAGTCTGGGGATTAG
Found at i:55955390 original size:23 final size:25
Alignment explanation
Indices: 55955339--55955390 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
55955329 AATCCTACCA
*
55955339 ACCAACCTCTACACACCATATCCGT
1 ACCAACCTCTACACACCATAGCCGT
55955364 -CCAACC-CTACACACCAT-GCCGT
1 ACCAACCTCTACACACCATAGCCGT
55955386 ACCAA
1 ACCAA
55955391 AATGCGGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 15 0.60
24 6 0.24
ACGTcount: A:0.33, C:0.46, G:0.06, T:0.15
Consensus pattern (25 bp):
ACCAACCTCTACACACCATAGCCGT
Found at i:55958181 original size:21 final size:20
Alignment explanation
Indices: 55958140--55958181 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
55958130 CCTGTTATCC
*
55958140 AATAAAAACCTAAGATTCCT
1 AATAAAAACCTAAAATTCCT
55958160 AATAATAAACC-AAAATTACCT
1 AATAA-AAACCTAAAATT-CCT
55958181 A
1 A
55958182 TCCGATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.55, C:0.19, G:0.02, T:0.24
Consensus pattern (20 bp):
AATAAAAACCTAAAATTCCT
Found at i:55958822 original size:22 final size:22
Alignment explanation
Indices: 55958796--55958839 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
55958786 TTATCTCTTT
55958796 TGATTGAAAAGGAGCAATAAAA
1 TGATTGAAAAGGAGCAATAAAA
55958818 TGATTGAAAAGGAGCAATAAAA
1 TGATTGAAAAGGAGCAATAAAA
55958840 AAATCGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.18
Consensus pattern (22 bp):
TGATTGAAAAGGAGCAATAAAA
Found at i:55961018 original size:21 final size:21
Alignment explanation
Indices: 55960994--55961037 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
55960984 ACGACCTAAT
*
55960994 TAAATAGAAAGGATA-ATTAAA
1 TAAATA-AAAGGATACAATAAA
*
55961015 TAAATAAAATGATACAATAAA
1 TAAATAAAAGGATACAATAAA
55961036 TA
1 TA
55961038 CTAAAGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (21 bp):
TAAATAAAAGGATACAATAAA
Found at i:55966040 original size:19 final size:19
Alignment explanation
Indices: 55966016--55966053 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55966006 TGGCTTAGAA
55966016 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
55966035 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
55966054 TTGGCTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:55972776 original size:27 final size:27
Alignment explanation
Indices: 55972737--55972789 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
55972727 AACTAGATCA
* *
55972737 ATTAAGAACAACACTTATTAAATAAAG
1 ATTAAAAAAAACACTTATTAAATAAAG
*
55972764 ATTAAAAAAAACACTTATTAATTAAA
1 ATTAAAAAAAACACTTATTAAATAAA
55972790 ACTAAGATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.28
Consensus pattern (27 bp):
ATTAAAAAAAACACTTATTAAATAAAG
Found at i:55973420 original size:13 final size:14
Alignment explanation
Indices: 55973402--55973454 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
55973392 TCTCTTCTTC
55973402 TTCTTTTCTTTTT-
1 TTCTTTTCTTTTTA
*
55973415 TTCTTTT-TTTTTC
1 TTCTTTTCTTTTTA
55973428 TTCTTGTTCTTTTTA
1 TTCTT-TTCTTTTTA
*
55973443 TT-TTCTCTTTTT
1 TTCTTTTCTTTTT
55973455 TTCACGAGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 5 0.14
13 19 0.54
14 4 0.11
15 7 0.20
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (14 bp):
TTCTTTTCTTTTTA
Found at i:55973430 original size:32 final size:32
Alignment explanation
Indices: 55973394--55973456 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
55973384 GTGCATATTC
*
55973394 TCTTCTTCTTCTTTTCT-TTTTTTCTTTTTTTT
1 TCTTCTTCTTCTTTT-TATTTTCTCTTTTTTTT
*
55973426 TCTTCTTGTTCTTTTTATTTTCTCTTTTTTT
1 TCTTCTTCTTCTTTTTATTTTCTCTTTTTTT
55973457 CACGAGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (32 bp):
TCTTCTTCTTCTTTTTATTTTCTCTTTTTTTT
Found at i:55973437 original size:19 final size:19
Alignment explanation
Indices: 55973405--55973448 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
55973395 CTTCTTCTTC
*
55973405 TTTTCTTTTTTTCTTTTT-
1 TTTTCTTTTGTTCTTTTTA
55973423 TTTTCTTCTTGTTCTTTTTA
1 TTTTCTT-TTGTTCTTTTTA
55973443 TTTTCT
1 TTTTCT
55973449 CTTTTTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 10 0.43
20 6 0.26
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (19 bp):
TTTTCTTTTGTTCTTTTTA
Found at i:55979605 original size:34 final size:34
Alignment explanation
Indices: 55979562--55979629 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
55979552 TCTCTTCTTA
55979562 CTTTTTGGTCAATTTCGCTGAATGAATCACAGGC
1 CTTTTTGGTCAATTTCGCTGAATGAATCACAGGC
*
55979596 CTTTTTGGTCAATTTCGCTTAATGAATCACAGGC
1 CTTTTTGGTCAATTTCGCTGAATGAATCACAGGC
55979630 AAAGTAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (34 bp):
CTTTTTGGTCAATTTCGCTGAATGAATCACAGGC
Found at i:55985367 original size:40 final size:40
Alignment explanation
Indices: 55985269--55985611 Score: 451
Period size: 40 Copynumber: 8.6 Consensus size: 40
55985259 TCCTCGTTCA
* * * ** *
55985269 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
55985308 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
55985348 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
55985388 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
55985428 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
55985468 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
55985508 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
55985548 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
55985588 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
55985612 CAGCATTCAA
Statistics
Matches: 279, Mismatches: 20, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
39 37 0.13
40 234 0.84
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:55993334 original size:39 final size:40
Alignment explanation
Indices: 55993289--55993460 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
55993279 GCTCCTCGTT
* * *
55993289 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
55993329 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
55993368 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
55993408 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
55993448 CAAATGCCTTCGG
1 CAAATGCCTTCGG
55993461 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:55993389 original size:40 final size:39
Alignment explanation
Indices: 55993291--55993513 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
55993281 TCCTCGTTCA
* * * *
55993291 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
55993330 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
55993369 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
55993409 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
55993449 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
55993490 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
55993514 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:55993473 original size:80 final size:79
Alignment explanation
Indices: 55993289--55993513 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
55993279 GCTCCTCGTT
* * * * *
55993289 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
55993353 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
55993368 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
55993433 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
55993448 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
55993512 GA
63 GA
55993514 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:55993522 original size:41 final size:41
Alignment explanation
Indices: 55993445--55993522 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
55993435 TTTGTATCTC
* * *
55993445 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
55993486 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
55993523 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:56005240 original size:14 final size:14
Alignment explanation
Indices: 56005221--56005248 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56005211 CTTCAAGGAA
56005221 TGATAAATTAATAT
1 TGATAAATTAATAT
56005235 TGATAAATTAATAT
1 TGATAAATTAATAT
56005249 AAGTCATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TGATAAATTAATAT
Found at i:56008905 original size:44 final size:42
Alignment explanation
Indices: 56008775--56008905 Score: 101
Period size: 44 Copynumber: 3.1 Consensus size: 42
56008765 ATGGTAAATC
* *
56008775 TTAATTTTAATTGATATATAAATGTAACACTAATTAAATTATAA
1 TTAATTTTAATTAATATAT-AATATAACACTAATT-AATTATAA
* * * * * *
56008819 TTAGTTTAAAGTAATATATAATA-ATACTCCAA-TAA-T-T-C
1 TTAATTTTAATTAATATATAATATA-ACACTAATTAATTATAA
*
56008857 TTAATTTTAATTTATATATAACTATAACACTAATTAAGTTATAA
1 TTAATTTTAATTAATATATAA-TATAACACTAATTAA-TTATAA
56008901 TTAAT
1 TTAAT
56008906 ATAGAATAAT
Statistics
Matches: 64, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
38 17 0.27
39 8 0.12
40 5 0.08
41 2 0.03
42 3 0.05
43 9 0.14
44 20 0.31
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (42 bp):
TTAATTTTAATTAATATATAATATAACACTAATTAATTATAA
Found at i:56008916 original size:82 final size:82
Alignment explanation
Indices: 56008773--56008923 Score: 223
Period size: 82 Copynumber: 1.8 Consensus size: 82
56008763 TAATGGTAAA
* * *
56008773 TCTTAATTTTAATTGATATATAAATGTAACACTAATTAAATTATAATTAGTTTAAAGTAATATAT
1 TCTTAATTTTAATTGATATATAAATATAACACTAATTAAATTATAATTAATATAAAGTAATATAT
56008838 AATAATACTCCAATAAT
66 AATAATACTCCAATAAT
* * * *
56008855 TCTTAATTTTAATTTATATATAACTATAACACTAATTAAGTTATAATTAATATAGAA-TAATATT
1 TCTTAATTTTAATTGATATATAAATATAACACTAATTAAATTATAATTAATATA-AAGTAATATA
56008919 TAATA
65 TAATA
56008924 TATAATATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
82 59 0.97
83 2 0.03
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (82 bp):
TCTTAATTTTAATTGATATATAAATATAACACTAATTAAATTATAATTAATATAAAGTAATATAT
AATAATACTCCAATAAT
Found at i:56008923 original size:17 final size:18
Alignment explanation
Indices: 56008896--56008935 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
56008886 CTAATTAAGT
*
56008896 TATAATTAATATAGAATA
1 TATATTTAATATAGAATA
*
56008914 -ATATTTAATATATAATA
1 TATATTTAATATAGAATA
56008931 TATAT
1 TATAT
56008936 AAAAAGCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TATATTTAATATAGAATA
Found at i:56009141 original size:26 final size:27
Alignment explanation
Indices: 56009089--56009141 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
56009079 AAGTAAAATT
* * *
56009089 AATTAATTTAGTCATATTCCTACTTAA
1 AATTAATATAGTCATATTACTAATTAA
*
56009116 AATTAATATA-TCATATTATTAATTAA
1 AATTAATATAGTCATATTACTAATTAA
56009142 TAAAATAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (27 bp):
AATTAATATAGTCATATTACTAATTAA
Found at i:56009274 original size:20 final size:20
Alignment explanation
Indices: 56009249--56009289 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
56009239 CTTACGCTTG
*
56009249 GGGCTTATAAGCTTTGATCA
1 GGGCTTATAAACTTTGATCA
56009269 GGGCTTATAAACTTTGATCA
1 GGGCTTATAAACTTTGATCA
56009289 G
1 G
56009290 TTTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (20 bp):
GGGCTTATAAACTTTGATCA
Found at i:56009870 original size:110 final size:109
Alignment explanation
Indices: 56009658--56009977 Score: 466
Period size: 110 Copynumber: 3.0 Consensus size: 109
56009648 ATTGAAATTC
* * * * * * *
56009658 AAAAGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGTACG-TTC
1 AAAAGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
* * *
56009720 CTCAAATTTCCAAATGCAAAACATTGCCTTATTTTGAAATTTTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTT
* * *
56009764 AAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCATCTTAGCGCATGTTTT
1 AAAAGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
56009829 CTCGAATTTCCCAAACGCAAAACATTGCCTTATTTTAAAATTTTT
66 CTCGAATTT-CCAAACGCAAAACATTGCCTTATTTTAAAATTTTT
*
56009874 AAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
1 AAAAGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
* *
56009939 CTCGAATTTCCAGACGCAAAACATTGCCTTATTTGAAAA
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAA
56009978 AAATTTCCTT
Statistics
Matches: 191, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
106 27 0.14
108 23 0.12
109 38 0.20
110 103 0.54
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (109 bp):
AAAAGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTT
Found at i:56012199 original size:95 final size:95
Alignment explanation
Indices: 56011943--56012224 Score: 503
Period size: 96 Copynumber: 3.0 Consensus size: 95
56011933 AAGATTTGAA
56011943 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
*
56012008 GTCACA-AGGAGGTAAAATCTGCCATCTTCG
66 ATCACAGA-GAGGTAAAATCTGCCATCTTCG
56012038 ATTCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGT
1 A-TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGT
56012103 AATCACAGAGAGGTAAAATCTGCCATCTTCG
65 AATCACAGAGAGGTAAAATCTGCCATCTTCG
* *
56012134 ATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATTGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
*
56012199 ATCACAGGGAGGTAAAATCTGCCATC
66 ATCACAGAGAGGTAAAATCTGCCATC
56012225 CTCAATCTGC
Statistics
Matches: 181, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
95 88 0.49
96 92 0.51
97 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
ATCACAGAGAGGTAAAATCTGCCATCTTCG
Found at i:56012359 original size:126 final size:126
Alignment explanation
Indices: 56012134--56012360 Score: 400
Period size: 126 Copynumber: 1.8 Consensus size: 126
56012124 GCCATCTTCG
* *
56012134 ATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATTGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTACTCCACTATA
56012199 ATCACAGGGAGGTAAAATCTGCCATCCTCAATCTGCTTCACTTTGGGAAATAAGATCTGAA
66 ATCACAGGGAGGTAAAATCTGCCATCCTCAATCTGCTTCACTTTGGGAAATAAGATCTGAA
*
56012260 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTATA
1 ATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTACTCCACTATA
* * *
56012325 GTCACAGGGAGGTAAAATCTGCCATCTTTAATCTGC
66 ATCACAGGGAGGTAAAATCTGCCATCCTCAATCTGC
56012361 AATCTATTCC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 95 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (126 bp):
ATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTACTCCACTATA
ATCACAGGGAGGTAAAATCTGCCATCCTCAATCTGCTTCACTTTGGGAAATAAGATCTGAA
Found at i:56012409 original size:95 final size:95
Alignment explanation
Indices: 56012259--56012447 Score: 324
Period size: 95 Copynumber: 2.0 Consensus size: 95
56012249 TAAGATCTGA
*
56012259 AATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTAT
1 AATCTGCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTAT
*
56012324 AGTCACAGGGAGGTAAAATCTGCCATCTTT
66 AGTCACAGGGAGGTAAAATCTGACATCTTT
* * *
56012354 AATCTGCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTTAATGTACTCTACTGT
1 AATCTGCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTAT
*
56012419 AGTCATAGGGAGGTAAAATCTGACATCTT
66 AGTCACAGGGAGGTAAAATCTGACATCTT
56012448 CGATCTGCTC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 88 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (95 bp):
AATCTGCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTAT
AGTCACAGGGAGGTAAAATCTGACATCTTT
Found at i:56012485 original size:38 final size:38
Alignment explanation
Indices: 56012425--56012500 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
56012415 CTGTAGTCAT
* * * *
56012425 AGGGAGGTAAAATCTGACATCTTCGATCTGCTCCACTG
1 AGGGAGATAAAATCTGAAATCTTCAATCTACTCCACTG
* * *
56012463 AGGGAGATAAGATTTGAAATCTTCAATCTATTCCACTG
1 AGGGAGATAAAATCTGAAATCTTCAATCTACTCCACTG
56012501 TCAACTAGGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (38 bp):
AGGGAGATAAAATCTGAAATCTTCAATCTACTCCACTG
Found at i:56012580 original size:126 final size:126
Alignment explanation
Indices: 56012354--56012581 Score: 357
Period size: 126 Copynumber: 1.8 Consensus size: 126
56012344 TGCCATCTTT
* * *
56012354 AATCTGCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTTAATGTACTCTACTGT
1 AATCTGCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTAT
* * *
56012419 AGTCATAGGGAGGTAAAATCTGACATCTTCGATCTGCTCCACTGAGGGAGATAAGATTTGA
66 AGTCACAGGGAGGGAAAATCTGACATCTTCAATCTGCTCCACTGAGGGAGATAAGATTTGA
* * *
56012480 AATCTTCAATCTATTCCACTGTCAACTAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTAT
1 AATCTGCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTAT
* *
56012545 AGTCACAGGGAGGGAAAATCTGCCATCTTTAATCTGC
66 AGTCACAGGGAGGGAAAATCTGACATCTTCAATCTGC
56012582 AATCTATTCC
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
126 91 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (126 bp):
AATCTGCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTAT
AGTCACAGGGAGGGAAAATCTGACATCTTCAATCTGCTCCACTGAGGGAGATAAGATTTGA
Found at i:56012598 original size:316 final size:304
Alignment explanation
Indices: 56011925--56012769 Score: 952
Period size: 316 Copynumber: 2.7 Consensus size: 304
56011915 AGCTCCACTT
* *
56011925 AGGGAGATAAGATTTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCT
1 AGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCT
* *
56011990 TCAATGTACTCCACTGTAGTCACAAGGAGGTAAAATCTGCCATCTTCGATTCTTCAATCTATTCC
66 TCAATGTACTCCACTGTAGTCACAAGGAGGTAAAATCTGCCATCTTC-AATCTACAATCTATTCC
* * * *
56012055 ACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCACAGAGAGGTAAA
130 ACTGCCAACCAGGGAGATAGAATTATCGGCTTTAATGTACTCTACTGTAGTCACAGGGAGGTAAA
* * *
56012120 ATCTGCCATCTTCGATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATTGGCTTCAA
195 ATCTGACATCTTCGATC-T--AGC--TTCCACTG-----CAGAGAGATAGAATTAAT-GCTTCAA
* * * * * **
56012185 TGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCCTCAATCTGCTTCACTT
249 TCTACTCCACTGTAATCACAGGGAGATAAAATCGGCCATACTCAATATGC-TCACGG
*
56012242 TGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCT
1 AGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCT
* * * *
56012307 TCAATGTACTCCACTATAGTCACAGGGAGGTAAAATCTGCCATCTTTAATCTGCAATCTATTCCA
66 TCAATGTACTCCACTGTAGTCACAAGGAGGTAAAATCTGCCATCTTCAATCTACAATCTATTCCA
*
56012372 CTGCCAACCAGGGAGATAGAATTATCGGCTTTAATGTACTCTACTGTAGTCATAGGGAGGTAAAA
131 CTGCCAACCAGGGAGATAGAATTATCGGCTTTAATGTACTCTACTGTAGTCACAGGGAGGTAAAA
* * *
56012437 TCTGACATCTTCGATCT-GC-TCCACTG-AGGGAGATAAGATTTGAAAT-CTTCAATCTATTCCA
196 TCTGACATCTTCGATCTAGCTTCCACTGCAGAGAGAT-AGAATT--AATGCTTCAATCTACTCCA
* *
56012498 CTGTCAA-C-TAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTATAG-TCACAGGG
258 CTGT-AATCACAGGGAGATA-AA--ATCGGC--C-A--TACT-CAATAT-GCTCAC--GG
** ** * *
56012555 AGGGAAAATCTGCCATCTTTAATCTGCAATCTATTCCACTGCCAATCAGGGAGATAGAATTATCG
1 AGGG-AAATAAG--ATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCG
* * *
56012620 GCTTCAATGTACTCCACTGTAGTCACAAAGAGGTAAAATCAGCCATCTTCGATCTACAATCTATT
63 GCTTCAATGTACTCCACTGTAGTCACAAGGAGGTAAAATCTGCCATCTTCAATCTACAATCTATT
*
56012685 CCACTGCCAACCAGGGAGATAGAATTATCGG-TTTCAATTTACT-TCACTGTAGTCACAGGGAGG
128 CCACTGCCAACCAGGGAGATAGAATTATCGGCTTT-AATGTACTCT-ACTGTAGTCACAGGGAGG
* *
56012748 TAAAATCTGTCATCTTTGATCT
191 TAAAATCTGACATCTTCGATCT
56012770 CCAATCTATT
Statistics
Matches: 461, Mismatches: 46, Indels: 43
0.84 0.08 0.08
Matches are distributed among these distances:
303 15 0.03
304 25 0.05
305 2 0.00
306 7 0.02
308 1 0.00
309 8 0.02
311 7 0.02
312 5 0.01
313 4 0.01
314 5 0.01
315 5 0.01
316 271 0.59
317 106 0.23
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (304 bp):
AGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCT
TCAATGTACTCCACTGTAGTCACAAGGAGGTAAAATCTGCCATCTTCAATCTACAATCTATTCCA
CTGCCAACCAGGGAGATAGAATTATCGGCTTTAATGTACTCTACTGTAGTCACAGGGAGGTAAAA
TCTGACATCTTCGATCTAGCTTCCACTGCAGAGAGATAGAATTAATGCTTCAATCTACTCCACTG
TAATCACAGGGAGATAAAATCGGCCATACTCAATATGCTCACGG
Found at i:56012619 original size:95 final size:95
Alignment explanation
Indices: 56012481--56012963 Score: 711
Period size: 95 Copynumber: 5.1 Consensus size: 95
56012471 AAGATTTGAA
* * *
56012481 ATCTTCAATCTATTCCACTGTCAACTAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTATA
1 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
* *
56012546 GTCACAGGGAGGGAAAATCTGCCATCTTTA
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
* *
56012576 ATCTGCAATCTATTCCACTGCCAATCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
** * *
56012641 GTCACAAAGAGGTAAAATCAGCCATCTTCG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
* * * *
56012671 ATCTACAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGTTTCAATTTACTTCACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
*
56012736 GTCACAGGGAGGTAAAATCTGTCATCTTTG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
* * * *
56012766 ATCTCCAATCTATTCCATTGCCAACCAGTGAGATAGAATTATCGACTTCAATGTA---CACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
* *
56012828 GTCACAGGGAGGTAAAATCTGCCATATTCG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
*
56012858 ATCTTCAATCTATTCCACTGCCAATCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
* *
56012923 GTCACAGGGAGGTAAAATTTGTCATCTTTG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
*
56012953 ATCTTCGATCT
1 ATCTTCAATCT
56012964 GCTTCGCTGT
Statistics
Matches: 345, Mismatches: 40, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
92 84 0.24
95 261 0.76
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
GTCACAGGGAGGTAAAATCTGCCATCTTTG
Found at i:56012669 original size:221 final size:221
Alignment explanation
Indices: 56012040--56012674 Score: 1027
Period size: 221 Copynumber: 2.9 Consensus size: 221
56012030 CATCTTCGAT
* *
56012040 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTATAG
* ** * *
56012105 TCACAGAGAGGTAAAATCTGCCATCTTCGATCTTCAATCTATTCCACTGCCAACCAGAGAGATAG
66 TCACAGGGAGGTAAAATCTGCCATCTTTAATCTGCAATCTATTCCACTGCCAACCAGGGAGATAG
* * * *
56012170 AATTATTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCCTCAATCTGC
131 AATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGC
* **
56012235 TTCACTTTGGGAAATAAGATCTGAAA
196 TCCACTGAGGGAAATAAGATCTGAAA
56012261 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTATAG
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTATAG
56012326 TCACAGGGAGGTAAAATCTGCCATCTTTAATCTGCAATCTATTCCACTGCCAACCAGGGAGATAG
66 TCACAGGGAGGTAAAATCTGCCATCTTTAATCTGCAATCTATTCCACTGCCAACCAGGGAGATAG
* * * *
56012391 AATTATCGGCTTTAATGTACTCTACTGTAGTCATAGGGAGGTAAAATCTGACATCTTCGATCTGC
131 AATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGC
* *
56012456 TCCACTGAGGGAGATAAGATTTGAAA
196 TCCACTGAGGGAAATAAGATCTGAAA
* *
56012482 TCTTCAATCTATTCCACTGTCAACTAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTATAG
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTATAG
* *
56012547 TCACAGGGAGGGAAAATCTGCCATCTTTAATCTGCAATCTATTCCACTGCCAATCAGGGAGATAG
66 TCACAGGGAGGTAAAATCTGCCATCTTTAATCTGCAATCTATTCCACTGCCAACCAGGGAGATAG
** *
56012612 AATTATCGGCTTCAATGTACTCCACTGTAGTCACAAAGAGGTAAAATCAGCCATCTTCGATCT
131 AATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCT
56012675 ACAATCTATT
Statistics
Matches: 383, Mismatches: 31, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
221 383 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (221 bp):
TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTATAG
TCACAGGGAGGTAAAATCTGCCATCTTTAATCTGCAATCTATTCCACTGCCAACCAGGGAGATAG
AATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGC
TCCACTGAGGGAAATAAGATCTGAAA
Found at i:56013107 original size:88 final size:88
Alignment explanation
Indices: 56012954--56013444 Score: 784
Period size: 88 Copynumber: 5.6 Consensus size: 88
56012944 TCATCTTTGA
* * ** * *
56012954 TCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAAATCTACTGCCTTCAACCAGCTCCACTAC
1 TCTTCGATCTGCTTCACTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
56013019 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* ** *
56013042 TCTTCGATCTACTTCACTGTCAATGTAGGAAGGCAAGATCTGTTGTCTTCAACTAGCTCCGCTAC
1 TCTTCGATCTGCTTCACTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
56013107 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* ** *
56013130 TCTTCGATCTACTTCACTGTCAATGTAGGAAGGCAAGATCTGTTGTCTTCAACTAGCTCCGCTAC
1 TCTTCGATCTGCTTCACTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
56013195 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* * *
56013218 TCTTCGATCTGCTTCACTGTCAATACAGGAAAGCAAGATTTGTTGTCTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCACTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
*
56013283 AACCAAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* * *
56013306 TCTTCGATCTGCATCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
1 TCTTCGATCTGCTTCACTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
56013371 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
*
56013394 TCTTCGATCTGCTTCACTGTCAATACAGGAAGACAAGATCTGTTGTCTTCA
1 TCTTCGATCTGCTTCACTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCA
56013445 TTAATCTGTT
Statistics
Matches: 374, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 374 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (88 bp):
TCTTCGATCTGCTTCACTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
AACCGAGAGAGGCAAGGTTTGTG
Found at i:56013120 original size:44 final size:44
Alignment explanation
Indices: 56013000--56013398 Score: 222
Period size: 44 Copynumber: 9.1 Consensus size: 44
56012990 AATCTACTGC
* * *
56013000 CTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG-TGT
1 CTTCAACTAGCTCCGCTACAACCGAGAGAGGCAAGATTTGTTGT
* * * * * *
56013043 CTTCGATCTA-CTTCACTGTCAA-TGTAG-GAAGGCAAGATCTGTTGT
1 CTTC-AACTAGCTCCGCT-ACAACCG-AGAG-AGGCAAGATTTGTTGT
*
56013088 CTTCAACTAGCTCCGCTACAACCGAGAGAGGCAAGGTTTG-TGT
1 CTTCAACTAGCTCCGCTACAACCGAGAGAGGCAAGATTTGTTGT
* * * * * *
56013131 CTTCGATCTA-CTTCACTGTCAA-TGTAG-GAAGGCAAGATCTGTTGT
1 CTTC-AACTAGCTCCGCT-ACAACCG-AGAG-AGGCAAGATTTGTTGT
*
56013176 CTTCAACTAGCTCCGCTACAACCGAGAGAGGCAAGGTTTG-TGT
1 CTTCAACTAGCTCCGCTACAACCGAGAGAGGCAAGATTTGTTGT
* * * * * *
56013219 CTTCGATCT-GCTTCACTGTCAATAC-AG-GAAAGCAAGATTTGTTGT
1 CTTC-AACTAGCTCCGCT-ACAA-CCGAGAG-AGGCAAGATTTGTTGT
* * * *
56013264 CTTCAACCAGCTCTGCTACAACCAAGAGAGGCAAGGTTTG-TGT
1 CTTCAACTAGCTCCGCTACAACCGAGAGAGGCAAGATTTGTTGT
* * * *
56013307 CTTCGATCT-GCAT-CGCTGTCAA-TGCAG-GAAGGCAAGATCTGTTGT
1 CTTC-AACTAGC-TCCGCT-ACAACCG-AGAG-AGGCAAGATTTGTTGT
* *
56013352 CTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTG-TGT
1 CTTCAACTAGCTCCGCTACAACCGAGAGAGGCAAGATTTGTTGT
56013395 CTTC
1 CTTC
56013399 GATCTGCTTC
Statistics
Matches: 264, Mismatches: 58, Indels: 68
0.68 0.15 0.17
Matches are distributed among these distances:
43 61 0.23
44 146 0.55
45 57 0.22
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (44 bp):
CTTCAACTAGCTCCGCTACAACCGAGAGAGGCAAGATTTGTTGT
Found at i:56014531 original size:21 final size:21
Alignment explanation
Indices: 56014505--56014550 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
56014495 GGTATAGCAA
56014505 GATCACCAAATGCCCCAATCT
1 GATCACCAAATGCCCCAATCT
*** *
56014526 GATCACTTCATGCCCCATTCT
1 GATCACCAAATGCCCCAATCT
56014547 GATC
1 GATC
56014551 TACAATTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.37, G:0.11, T:0.26
Consensus pattern (21 bp):
GATCACCAAATGCCCCAATCT
Found at i:56014648 original size:6 final size:6
Alignment explanation
Indices: 56014637--56014675 Score: 50
Period size: 5 Copynumber: 7.2 Consensus size: 6
56014627 TTGGCCTCTC
56014637 CTTTTT CTTTTT C-TTTT -TTTTT C-TTTT -TTTTT CTTTTT C
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C
56014676 AAAATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 16 0.55
6 13 0.45
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
CTTTTT
Found at i:56014659 original size:10 final size:10
Alignment explanation
Indices: 56014639--56014674 Score: 63
Period size: 10 Copynumber: 3.5 Consensus size: 10
56014629 GGCCTCTCCT
56014639 TTTTCTTTTTC
1 TTTT-TTTTTC
56014650 TTTTTTTTTC
1 TTTTTTTTTC
56014660 TTTTTTTTTC
1 TTTTTTTTTC
56014670 TTTTT
1 TTTTT
56014675 CAAAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 21 0.84
11 4 0.16
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:56014659 original size:16 final size:17
Alignment explanation
Indices: 56014637--56014675 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
56014627 TTGGCCTCTC
56014637 CTTTTTCTTTTTCTTTT
1 CTTTTTCTTTTTCTTTT
56014654 -TTTTTCTTTTT-TTTT
1 CTTTTTCTTTTTCTTTT
56014669 CTTTTTC
1 CTTTTTC
56014676 AAAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
CTTTTTCTTTTTCTTTT
Found at i:56018606 original size:110 final size:110
Alignment explanation
Indices: 56018401--56018721 Score: 429
Period size: 111 Copynumber: 2.9 Consensus size: 110
56018391 ATTGAAATTC
* * * * * * * * *
56018401 AAAAGGATATTTGGCTATTTGATTAAAC-GAGAAATCGAAACCCAGCACCTTAGGGTACG-TTCC
1 AAAAGGATATTTAGCCATTTGGTTGAACAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTC
*
56018464 TCAAATTTCCAAACGCAAAACATTGTCTTATTTTGAAAA-TTTT-
66 TCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTTA
56018507 AAAAGGATATTTAGCCATTTGGTTGAATCAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
1 AAAAGGATATTTAGCCATTTGGTTGAA-CAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
* *
56018572 CTCGAATTTCCCAAATGCAAAACATTGCCTTATTTT-AAAATTTTTA
65 CTCAAATTT-CCAAACGCAAAACATTGCCTTATTTTGAAAATTTTTA
* *
56018618 AAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCGACACCTAGCACCTTAGGGCATGTTTT
1 AAAAGGATATTTAGCCATTTGGTTGAAC-AGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
* *
56018683 CTCAAATTTCCAGACACAAAACATTGCCTTA-TTTGAAAA
65 CTCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAA
56018722 AAAATTCCTT
Statistics
Matches: 189, Mismatches: 18, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
106 23 0.12
107 1 0.01
108 27 0.14
109 17 0.09
110 52 0.28
111 69 0.37
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (110 bp):
AAAAGGATATTTAGCCATTTGGTTGAACAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTC
TCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTTA
Found at i:56019074 original size:3 final size:3
Alignment explanation
Indices: 56019066--56019112 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
56019056 ATATAAAAGC
56019066 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT GAA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
56019110 AAT
1 AAT
56019113 GTTAAAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 36 0.88
4 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:56019753 original size:12 final size:12
Alignment explanation
Indices: 56019736--56019762 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56019726 AACATTTTTA
56019736 ATATATATATGT
1 ATATATATATGT
56019748 ATATATATATGT
1 ATATATATATGT
56019760 ATA
1 ATA
56019763 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATATATATGT
Found at i:56022417 original size:25 final size:24
Alignment explanation
Indices: 56022330--56022418 Score: 80
Period size: 25 Copynumber: 3.8 Consensus size: 24
56022320 TTTAAATTGA
*
56022330 TATTTAATAAATTATAAAAATATAT
1 TATTTAAT-AATTTTAAAAATATAT
*
56022355 TATTT-AT--TTTT-AATATATATT
1 TATTTAATAATTTTAAAAATATA-T
*
56022376 TTTTTAA-AATTTGTAAAAATATAT
1 TATTTAATAATTT-TAAAAATATAT
56022400 TATTTAATGAATTTTAAAA
1 TATTTAAT-AATTTTAAAA
56022419 GTAAATGTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
20 7 0.14
21 8 0.16
22 1 0.02
23 3 0.06
24 10 0.20
25 17 0.33
26 5 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTTAATAATTTTAAAAATATAT
Found at i:56022827 original size:32 final size:33
Alignment explanation
Indices: 56022790--56022857 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 33
56022780 TTTAAAAATT
56022790 TATTTTAAGAT-AATTTATC-AAAC-TGTGAAAAA
1 TATTTT-AGATAAATTTATCTAAACAT-TGAAAAA
**
56022822 TATTTTTTATAAATTTATCTAAACATTGAAAAA
1 TATTTTAGATAAATTTATCTAAACATTGAAAAA
56022855 TAT
1 TAT
56022858 ATATTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 2 0.06
32 14 0.45
33 14 0.45
34 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (33 bp):
TATTTTAGATAAATTTATCTAAACATTGAAAAA
Found at i:56023204 original size:29 final size:30
Alignment explanation
Indices: 56023155--56023222 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
56023145 TTTTCCGAAA
56023155 TTTAGAATTTAGTTTGGATA-TTTTTAT-T
1 TTTAGAATTTAGTTTGGATATTTTTTATAT
*
56023183 TTTAGGAATTTAGTCTT-TATATTTTTTATAT
1 TTTA-GAATTTAGT-TTGGATATTTTTTATAT
56023214 TTTA-AATTT
1 TTTAGAATTT
56023223 CAGATTCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
28 4 0.11
29 17 0.49
30 9 0.26
31 5 0.14
ACGTcount: A:0.26, C:0.01, G:0.10, T:0.62
Consensus pattern (30 bp):
TTTAGAATTTAGTTTGGATATTTTTTATAT
Found at i:56024596 original size:15 final size:15
Alignment explanation
Indices: 56024578--56024607 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56024568 GATGTAATTA
56024578 TAAATCTTTATATTT
1 TAAATCTTTATATTT
*
56024593 TAAATGTTTATATTT
1 TAAATCTTTATATTT
56024608 CAATATAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (15 bp):
TAAATCTTTATATTT
Found at i:56040257 original size:80 final size:80
Alignment explanation
Indices: 56040124--56040282 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 80
56040114 CTATCTTACA
**
56040124 TAGTGGACTATTTGCATCATAAAACCTTTTATTTATAAAGAAAACCACTATTCGACCCTTTTAAA
1 TAGTGGACTATTTGCATCATAAAACCTCCTATTTATAAAGAAAACCACTATTCGACCCTTTTAAA
*
56040189 AATAACCATCTAATG
66 AATAACCACCTAATG
* * * *
56040204 TAGTGGGCTATTTTCATCATAAAACCTCCTATTTATAAAGACAACCACTATTCGGCCCTTTTAAA
1 TAGTGGACTATTTGCATCATAAAACCTCCTATTTATAAAGAAAACCACTATTCGACCCTTTTAAA
56040269 AATAACCACCTAAT
66 AATAACCACCTAAT
56040283 TTTTTATTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (80 bp):
TAGTGGACTATTTGCATCATAAAACCTCCTATTTATAAAGAAAACCACTATTCGACCCTTTTAAA
AATAACCACCTAATG
Found at i:56043889 original size:12 final size:13
Alignment explanation
Indices: 56043862--56043886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56043852 ATTAAAATAT
56043862 TTTTTTATAAAAA
1 TTTTTTATAAAAA
56043875 TTTTTTATAAAA
1 TTTTTTATAAAA
56043887 TTTAATGGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTTATAAAAA
Found at i:56043898 original size:14 final size:14
Alignment explanation
Indices: 56043881--56043913 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
56043871 AAAATTTTTT
56043881 ATAAAATTTAATGG
1 ATAAAATTTAATGG
56043895 ATAAAATTTAATGG
1 ATAAAATTTAATGG
56043909 ATAAA
1 ATAAA
56043914 TAAAAGTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (14 bp):
ATAAAATTTAATGG
Found at i:56044861 original size:20 final size:21
Alignment explanation
Indices: 56044836--56044882 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
56044826 ATTTAAAAAC
56044836 AAATAACATATAAAAA-TTTA
1 AAATAACATATAAAAAGTTTA
* *
56044856 AAATAATATGTAAAAAGTTTA
1 AAATAACATATAAAAAGTTTA
56044877 AAATAA
1 AAATAA
56044883 ATAATATGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
AAATAACATATAAAAAGTTTA
Found at i:56044864 original size:18 final size:19
Alignment explanation
Indices: 56044843--56044886 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
56044833 AACAAATAAC
56044843 ATATAAAAA-TTTAAAATA
1 ATATAAAAAGTTTAAAATA
56044861 ATATGTAAAAAGTTTAAAATA
1 ATA--TAAAAAGTTTAAAATA
56044882 A-ATAA
1 ATATAA
56044887 TATGTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 6 0.26
20 7 0.30
21 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
ATATAAAAAGTTTAAAATA
Found at i:56045031 original size:23 final size:25
Alignment explanation
Indices: 56044977--56045031 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
56044967 ACAATTCCAA
*
56044977 ATAAATAATATACATATGTACTTTAAT
1 ATAAATAATATACATA-GTAC-TAAAT
56045004 ATAAATAATATACATA-TA-TAAAT
1 ATAAATAATATACATAGTACTAAAT
*
56045027 TTAAA
1 ATAAA
56045032 ATGAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 8 0.31
25 2 0.08
27 16 0.62
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (25 bp):
ATAAATAATATACATAGTACTAAAT
Found at i:56045128 original size:21 final size:20
Alignment explanation
Indices: 56045104--56045144 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
56045094 AACAGAACAA
56045104 TTTAAAATAAATAATATAAAT
1 TTTAAAATAAATAA-ATAAAT
56045125 TTTAAAATAAATAAATAAAT
1 TTTAAAATAAATAAATAAAT
56045145 AAATTGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTAAAATAAATAAATAAAT
Found at i:56045156 original size:25 final size:25
Alignment explanation
Indices: 56045108--56045160 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
56045098 GAACAATTTA
**
56045108 AAATAAATAATATAAATTTTAAAAT
1 AAATAAATAATATAAATTCAAAAAT
56045133 AAATAAATAA-ATAAATTGCAAAAAT
1 AAATAAATAATATAAATT-CAAAAAT
56045158 AAA
1 AAA
56045161 GTGAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (25 bp):
AAATAAATAATATAAATTCAAAAAT
Found at i:56046942 original size:44 final size:44
Alignment explanation
Indices: 56046781--56047722 Score: 322
Period size: 44 Copynumber: 21.8 Consensus size: 44
56046771 AGATTCATCG
* * * *
56046781 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TAATAG-
1 TTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCT-GT-GT
* * * * * *
56046825 CTTCAATATGCTCCGCTGTAACTTCAGGGAGATAAGAT-TG-G-
1 TTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTGT
*** * **
56046866 TTGCGATCTGCTCTACCACAACTTC-AGAGAGATAAGATCTGTGT
1 TTTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATCTGTGT
* * *
56046910 TTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGAT-TGAT-T
1 TTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTG-TGT
* * * * * * * *
56046953 TCTTCT-GTCTGTTGCACTGTAACTTGAGGGATATAATAT-TG-G-
1 T-TT-TAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTGT
*** * * *
56046995 TTGCGATCTTCTCTACTGCAACTTC-AGAGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATCTGTGT
* * * *
56047039 TTTTAATCCGCTTCACTGCAACTT-TAGAGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATCTGTGT
*
56047083 TTTTAATCTGCTTCACTGCAACTTCAAGGAGAT-AGAAT-TGAT-T
1 TTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAG-ATCTG-TGT
** * * *
56047126 TCTTTCGTCTGTTCCACTGTAACTTCAGGGAGATAAGA-CTG-G-
1 T-TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTGT
* *** * * *
56047168 ATGCGATTTGCTCTACTGCAACTTC-AGGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTGT
* * * * *
56047211 TTTTAATCCGCTCAACTACAACTTCAGGGAGATAGGAT-TG-GTT
1 TTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTG-T
** * * * *
56047254 TCTTTTGTCTTCTCCATTACAACTTC-AGAGAGATAA-AACTG-G-
1 T-TTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATCTGTGT
* * * * * * * * *
56047296 ATGTGATCTACTCTACTGCAACTTC-AGAAAGATAATATTTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATCTGTGT
* * *
56047340 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TG-GTT
1 TTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTG-T
** * *
56047383 TCTTTTGTCTGCTCCATTGCAACTTCAGGGAGATAAGA-CTG-G-
1 T-TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTGT
* * * * * * *
56047425 ATGTGATTTGCTCTACTGCAACTTC-AGAGAGATAAGATATGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATCTGTGT
* *
56047469 TTTTAATTTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GT
1 TTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTGT
* * *
56047511 TTCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGT-TG-GTT
1 TT-TT-AATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTG-T
* * ** * *
56047556 TTCTTCAGTCTGCTCCACTACTGCTT-AGGGAGATAATA-CT-TG-
1 TT-TT-AATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTGT
* *** * *
56047598 ATGCGATCTACTCTACTGCAACTTC-AGAGAGATAAGATCTGTAG-
1 TTTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATCTGT-GT
* * * * * *
56047642 TTTTAATCCGCTCCATTCCAACTTCAGGGAGATAGGGT-TG-GTT
1 TTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTG-T
**
56047685 TCTTTTGTCTGCTCCACTGCAACTTC-AGAGAGATAAGA
1 T-TTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGA
56047723 CTGGATGTGA
Statistics
Matches: 663, Mismatches: 178, Indels: 114
0.69 0.19 0.12
Matches are distributed among these distances:
40 27 0.04
41 130 0.20
42 19 0.03
43 47 0.07
44 408 0.62
45 32 0.05
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (44 bp):
TTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCTGTGT
Found at i:56047018 original size:85 final size:82
Alignment explanation
Indices: 56046924--56047200 Score: 204
Period size: 85 Copynumber: 3.2 Consensus size: 82
56046914 AATCCGCTCC
*
56046924 ACTGTAACTTCAAGGAGATAGGATTGATTTCTTCTGTCTGTTGCACTGTAACTTGAGGGATATAA
1 ACTGCAACTTC-AGGAGATAGGATTGATTTCTT-TGTCTGTT-CACTGTAACTTGAGGGATATAA
56046989 TATTGGTTGCGATCTTCTCT
63 TATTGGTTGCGATCTTCTCT
* ** * * *
56047009 ACTGCAACTTCAGAGAGATAAGATCTG-TGGTT-TTAATCCGCTTCACTGCAACTTTAGAGAGAT
1 ACTGCAACTTCAG-GAGATAGGAT-TGAT--TTCTTTGTCTG-TTCACTGTAAC-TT-GAGGGAT
* *** *
56047072 A-AGATCTGTGGTTTTAATCTGCT-T
59 ATA-ATAT-TGGTTGCGATCTTCTCT
* * *
56047096 CACTGCAACTTCAAGGAGATAGAATTGATTTCTTTCGTCTGTTCCACTGTAACTTCAGGGAGATA
1 -ACTGCAACTTC-AGGAGATAGGATTGATTTCTTT-GTCTGTT-CACTGTAACTTGAGGGATATA
* * *
56047161 AGACTGGATGCGAT-TTGCTCT
62 ATATTGGTTGCGATCTT-CTCT
56047182 ACTGCAACTTCAGGAGATA
1 ACTGCAACTTCAGGAGATA
56047201 AGATCTGTGG
Statistics
Matches: 145, Mismatches: 29, Indels: 37
0.69 0.14 0.18
Matches are distributed among these distances:
84 11 0.08
85 50 0.34
86 18 0.12
87 22 0.15
88 42 0.29
89 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (82 bp):
ACTGCAACTTCAGGAGATAGGATTGATTTCTTTGTCTGTTCACTGTAACTTGAGGGATATAATAT
TGGTTGCGATCTTCTCT
Found at i:56047070 original size:173 final size:172
Alignment explanation
Indices: 56046883--56047244 Score: 541
Period size: 173 Copynumber: 2.1 Consensus size: 172
56046873 CTGCTCTACC
* * *
56046883 ACAACTTCAGAGAGATAAGATCTGTGTTTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGAT
1 ACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGAAT
* * * * * *
56046948 TGATTTC-TTCTGTCTGTTGCACTGTAACTTGAGGGATATAATATTGGTTGCGATCTT-CTCTAC
66 TGATTTCTTTC-GTCTGTTCCACTGTAACTTCAGGGAGATAAGACTGGATGCGAT-TTGCTCTAC
56047011 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTTC-ACT
129 TGCAACTTCAG-GAGATAAGATCTGTGGTTTTAATCCGC-TCAACT
* * * *
56047056 GCAACTTTAGAGAGATAAGATCTGTGGTTTTAATCTGCTTCACTGCAACTTCAAGGAGATAGAAT
1 ACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGAAT
56047121 TGATTTCTTTCGTCTGTTCCACTGTAACTTCAGGGAGATAAGACTGGATGCGATTTGCTCTACTG
66 TGATTTCTTTCGTCTGTTCCACTGTAACTTCAGGGAGATAAGACTGGATGCGATTTGCTCTACTG
56047186 CAACTTCAGGAGATAAGATCTGTGGTTTTAATCCGCTCAACT
131 CAACTTCAGGAGATAAGATCTGTGGTTTTAATCCGCTCAACT
*
56047228 ACAACTTCAGGGAGATA
1 ACAACTTCAGAGAGATA
56047245 GGATTGGTTT
Statistics
Matches: 170, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
171 2 0.01
172 46 0.27
173 119 0.70
174 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (172 bp):
ACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGAAT
TGATTTCTTTCGTCTGTTCCACTGTAACTTCAGGGAGATAAGACTGGATGCGATTTGCTCTACTG
CAACTTCAGGAGATAAGATCTGTGGTTTTAATCCGCTCAACT
Found at i:56047100 original size:129 final size:127
Alignment explanation
Indices: 56046749--56047548 Score: 441
Period size: 129 Copynumber: 6.2 Consensus size: 127
56046739 TTAATCAGAC
* * *
56046749 CTACTGCAACTTCAGAG-GTATAAGAT-TCATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAG
1 CTACTGCAACTTCAGAGAG-ATAAGATCT-GTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAG
* * * * * *
56046812 ATAGGATTAATAGCTTCAATATGCTCCGCTGTAACTTCAGGGAGATAAGATTGGTTGCGATCTGC
64 ATAGGATT-GT-GTTTTAATCTGCTTCACTGTAACTTCAGGGAGATAAGATTGGTTGCGATCTGC
56046877 T
127 T
** * *
56046878 CTACCACAACTTCAGAGAGATAAGATCTGTGTTTTTAATCCGCTCCACTGTAACTTCA-AGGAGA
1 CTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGA-GAGA
** * * * *
56046942 TAGGATTGAT-TTCTTCTGTCTG-TTGCACTGTAACTTGAGGGATATAATATTGGTTGCGATCTT
65 TAGGATTG-TGTT-TT-AATCTGCTT-CACTGTAACTTCAGGGAGATAAGATTGGTTGCGATCTG
56047005 CT
126 CT
* *
56047007 CTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTTCACTGCAACTTTAGAGAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGAT
* * * ** *
56047072 AAGATCTGTGGTTTTAATCTGCTTCACTGCAACTTCAAGGAGATAGAATTGATTTCTTTCG-TCT
66 AGGAT-TGT-GTTTTAATCTGCTTCACTGTAACTTCAGGGAGAT--AA--GATTGGTTGCGATCT
*
56047136 GTT
125 GCT
* * * * *** ** *
56047139 CCACTGTAACTTCAGGGAGATAAGA-C--TGGATGCGATTTGCTCTACTGCAACTTCAG-GAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGAT
* * ** * *
56047200 AAGATCTGTGGTTTTAATCCGC-TCAACTACAACTTCAGGGAGATAGGATTGGTTTCTTTTG-TC
66 AGGAT-TGT-GTTTTAATCTGCTTC-ACTGTAACTTCAGGGAGATAAGATTGGTTGC----GATC
*
56047263 TTCT
124 TGCT
* * * * * * * ** * *
56047267 CCATTACAACTTCAGAGAGATAA-AAC--TGGATGTGATCTACTCTACTGCAACTTCAGAAAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGAT
** * * * * *
56047329 AATATTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTG-TCT
66 AGGA-TTGT-GTTTTAATCTGCTTCACTGTAACTTCAGGGAGATAAGATTGGTTGC----GATCT
56047393 GCT
125 GCT
* * * * * * ** *
56047396 CCATTGCAACTTCAGGGAGATAAGA-C--TGGATGTGATTTGCTCTACTGCAACTTCAGAGAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGAT
* * * * * * *
56047458 AAGATATGTGGTTTTAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCAACCTG
66 AGGAT-TGT-GTTTTAATCTGCTTCACTGTAACTTCAGGGAGATAAGATTGG--T-TGCGATCTG
56047523 CT
126 CT
* *
56047525 CCACTGCAACTTCAGGGAGATAAG
1 CTACTGCAACTTCAGAGAGATAAG
56047549 GTTGGTTTTC
Statistics
Matches: 558, Mismatches: 82, Indels: 62
0.79 0.12 0.09
Matches are distributed among these distances:
124 8 0.01
126 1 0.00
127 4 0.01
128 98 0.18
129 393 0.70
130 12 0.02
131 6 0.01
132 29 0.05
133 7 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (127 bp):
CTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGAT
AGGATTGTGTTTTAATCTGCTTCACTGTAACTTCAGGGAGATAAGATTGGTTGCGATCTGCT
Found at i:56047489 original size:173 final size:173
Alignment explanation
Indices: 56047310--56047721 Score: 465
Period size: 173 Copynumber: 2.4 Consensus size: 173
56047300 GATCTACTCT
*
56047310 ACTGCAACTTCAGAAAGATAATATTTGTGGTT-TT-AATCC-GCTCCACTGCAACTTCAGGGAGA
1 ACTGCAACTTCAGAAAGATAAGA-TTG-GGTTCTTCAA-CCTGCTCCACTGCAACTTCAGGGAGA
** * * * * *
56047372 T-AGGATTGG-TTTCTTTTGTCTGCTCCATTGCAACTTCAGGGAGATAAGACTGGATGTGATTTG
63 TAAGG-TTGGTTTTCTTCAGTCTGCTCCACTACAACTT-AGGGAGATAAGACTGGATGCGATCTA
* **
56047435 CTCTACTGCAACTTCAGAGAGATAAGATATGTGGTTTTAATTTGCTCC
126 CTCTACTGCAACTTCAGAGAGATAAGATATGTAGTTTTAATCCGCTCC
** *
56047483 ACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAA
1 ACTGCAACTTCAGAAAGATAAGATTGGGTTCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAA
** * *
56047548 GGTTGGTTTTCTTCAGTCTGCTCCACTACTGCTTAGGGAGATAATACTTGATGCGATCTACTCTA
66 GGTTGGTTTTCTTCAGTCTGCTCCACTACAACTTAGGGAGATAAGACTGGATGCGATCTACTCTA
*
56047613 CTGCAACTTCAGAGAGATAAGATCTGTAGTTTTAATCCGCTCC
131 CTGCAACTTCAGAGAGATAAGATATGTAGTTTTAATCCGCTCC
* * ** * * * **** *
56047656 ATTCCAACTTCAGGGAGATAGGGTTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGAGAGATAA
1 ACTGCAACTTCAGAAAGATAAGATTGGGTTCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAA
56047721 G
66 G
56047722 ACTGGATGTG
Statistics
Matches: 206, Mismatches: 28, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
171 3 0.01
172 7 0.03
173 172 0.83
174 24 0.12
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (173 bp):
ACTGCAACTTCAGAAAGATAAGATTGGGTTCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAA
GGTTGGTTTTCTTCAGTCTGCTCCACTACAACTTAGGGAGATAAGACTGGATGCGATCTACTCTA
CTGCAACTTCAGAGAGATAAGATATGTAGTTTTAATCCGCTCC
Found at i:56047616 original size:129 final size:128
Alignment explanation
Indices: 56047483--56047769 Score: 339
Period size: 129 Copynumber: 2.2 Consensus size: 128
56047473 AATTTGCTCC
* *
56047483 ACTGCAACTTCAGGGAGATAAGAT-TGGT-TTCTTCAA-CCTGCTCCACTGCAACTTCAGGGAGA
1 ACTGCAACTTCAGAGAGATAAGATCT-GTATT-TT-AATCC-GCTCCACTCCAACTTCAGGGAGA
** * * * *
56047545 TAAGGTTGGTTTTCTTCAGTCTGCTCCACTACTGCTT-AGGGAGATAATACTTGATGCGATCTAC
62 TAAGGTTGG-TTTCTTCAGTCTGCTCCACTACAACTTCAGAGAGATAAGACTGGATGCGATATAC
56047609 TCT
126 TCT
* *
56047612 ACTGCAACTTCAGAGAGATAAGATCTGTAGTTTTAATCCGCTCCATTCCAACTTCAGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTA-TTTTAATCCGCTCCACTCCAACTTCAGGGAGATAA
** * * *
56047677 GGTTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGTGATATGCTCT
65 GGTTGGTTTCTTCAGTCTGCTCCACTACAACTTCAGAGAGATAAGACTGGATGCGATATACTCT
* *
56047741 ACTACAACTTCAGAGAGATAAGATATGTA
1 ACTGCAACTTCAGAGAGATAAGATCTGTA
56047770 ATGTATGGCT
Statistics
Matches: 136, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
128 22 0.16
129 107 0.79
130 5 0.04
131 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (128 bp):
ACTGCAACTTCAGAGAGATAAGATCTGTATTTTAATCCGCTCCACTCCAACTTCAGGGAGATAAG
GTTGGTTTCTTCAGTCTGCTCCACTACAACTTCAGAGAGATAAGACTGGATGCGATATACTCT
Found at i:56047866 original size:50 final size:50
Alignment explanation
Indices: 56047812--56047935 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
56047802 CGGGGGAAGC
* * *
56047812 AAGATTCGCTGTCGTAGCTTTAATCTG-CTCCACTGCACCGCCAGGAAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTC-CCACTACACCGCCAGGAAAGT
* * * *
56047862 AAGATTCACCGTTGTGGCTTCAATCTGTCCCACTACACCGCCAGGGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTCCCACTACACCGCCAGGAAAGT
* * *
56047912 AAAATTCGCCGTTGTGGCTTCAAT
1 AAGATTCGCCGTCGTAGCTTCAAT
56047936 ATTTTTAATT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 63 0.98
51 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGATTCGCCGTCGTAGCTTCAATCTGTCCCACTACACCGCCAGGAAAGT
Found at i:56048858 original size:17 final size:17
Alignment explanation
Indices: 56048832--56048865 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
56048822 CTTTTCCTTA
*
56048832 TTTTCTTTTCTTTTTTC
1 TTTTCGTTTCTTTTTTC
56048849 TTTTCGTTTCTTTTTTC
1 TTTTCGTTTCTTTTTTC
56048866 AAGTGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTCGTTTCTTTTTTC
Found at i:56052656 original size:26 final size:26
Alignment explanation
Indices: 56052618--56052749 Score: 114
Period size: 26 Copynumber: 5.2 Consensus size: 26
56052608 GTAAATAGTA
56052618 TAAAACAATTTAAAACAAATAATATG
1 TAAAACAATTTAAAACAAATAATATG
* **
56052644 TAAAACAAATTAAAATGAATAATAT-
1 TAAAACAATTTAAAACAAATAATATG
* * *
56052669 TCAAAGCAATTTAAAAACAAATAACATA
1 T-AAAACAATTT-AAAACAAATAATATG
*
56052697 TAAAAAAATTT---A-AAATAATATG
1 TAAAACAATTTAAAACAAATAATATG
* *
56052719 TAAAA-AGTTTAAAATAAATAATATG
1 TAAAACAATTTAAAACAAATAATATG
56052744 TCAAAA
1 T-AAAA
56052750 GGAATCTTAA
Statistics
Matches: 85, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
21 4 0.05
22 13 0.15
23 1 0.01
24 1 0.01
25 12 0.14
26 34 0.40
27 19 0.22
28 1 0.01
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.27
Consensus pattern (26 bp):
TAAAACAATTTAAAACAAATAATATG
Found at i:56052713 original size:22 final size:21
Alignment explanation
Indices: 56052687--56052735 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
56052677 ATTTAAAAAC
56052687 AAATAACATATAAAAAAATTTA
1 AAATAACATAT-AAAAAATTTA
* * *
56052709 AAATAATATGTAAAAAGTTTA
1 AAATAACATATAAAAAATTTA
56052730 AAATAA
1 AAATAA
56052736 ATAATATGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
AAATAACATATAAAAAATTTA
Found at i:56052944 original size:25 final size:26
Alignment explanation
Indices: 56052907--56052973 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 26
56052897 TTAACATAGT
**
56052907 TTAAAATGCATAATATATA-AAAAAC
1 TTAAAATAAATAATATATAGAAAAAC
* *
56052932 TTAAAATAAATAATA-ATAGAACAAT
1 TTAAAATAAATAATATATAGAAAAAC
56052957 TTAAAATAAATAATATA
1 TTAAAATAAATAATATA
56052974 AAGTTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 3 0.08
25 32 0.89
26 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (26 bp):
TTAAAATAAATAATATATAGAAAAAC
Found at i:56052947 original size:21 final size:21
Alignment explanation
Indices: 56052918--56053001 Score: 78
Period size: 25 Copynumber: 3.7 Consensus size: 21
56052908 TAAAATGCAT
*
56052918 AATATATAAAAAACTTAAAATA
1 AATA-ATAAAAAATTTAAAATA
56052940 AATAATAATAGAACAATTTAAAATA
1 AATAAT-A-A-AA-AATTTAAAATA
* *
56052965 AATAATATAAAGTTTAAAATA
1 AATAATAAAAAATTTAAAATA
56052986 AATAAATAAATAAATT
1 AAT-AATAAA-AAATT
56053002 GCAAAAATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
21 15 0.29
22 12 0.24
23 5 0.10
24 3 0.06
25 16 0.31
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAATAAAAAATTTAAAATA
Found at i:56052971 original size:22 final size:21
Alignment explanation
Indices: 56052939--56052990 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
56052929 AACTTAAAAT
56052939 AAAT-AATAATAGAACAATTTA
1 AAATAAATAATAGAA-AATTTA
* *
56052960 AAATAAATAATATAAAGTTTA
1 AAATAAATAATAGAAAATTTA
56052981 AAATAAATAA
1 AAATAAATAA
56052991 ATAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
AAATAAATAATAGAAAATTTA
Found at i:56054809 original size:31 final size:31
Alignment explanation
Indices: 56054738--56054810 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
56054728 TACATAAATA
56054738 ATCATTCAACTATTCAATTCATTTTATATTG
1 ATCATTCAACTATTCAATTCATTTTATATTG
* * * * *
56054769 ATCACTCAACTATT-ATTTTATTTTATTTTT
1 ATCATTCAACTATTCAATTCATTTTATATTG
56054799 AGTCATTCAACT
1 A-TCATTCAACT
56054811 TTTTGAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (31 bp):
ATCATTCAACTATTCAATTCATTTTATATTG
Found at i:56062368 original size:29 final size:29
Alignment explanation
Indices: 56062329--56062390 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
56062319 TAAAAATTAC
56062329 TAAAAACGGGCAAGGTTTACTTATCGAAT
1 TAAAAACGGGCAAGGTTTACTTATCGAAT
* *
56062358 TAAAAATGGGCAAGGTTTGCTTATCGAAT
1 TAAAAACGGGCAAGGTTTACTTATCGAAT
56062387 TAAA
1 TAAA
56062391 GAACCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (29 bp):
TAAAAACGGGCAAGGTTTACTTATCGAAT
Found at i:56063471 original size:10 final size:10
Alignment explanation
Indices: 56063456--56063486 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
56063446 AAAAAAGTAT
56063456 AATTTTTTTA
1 AATTTTTTTA
56063466 AATTTTTTT-
1 AATTTTTTTA
56063475 AATTTTTTTA
1 AATTTTTTTA
56063485 AA
1 AA
56063487 ATAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:56063483 original size:9 final size:9
Alignment explanation
Indices: 56063455--56063485 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
56063445 AAAAAAAGTA
56063455 TAATTTTTT
1 TAATTTTTT
56063464 TAAATTTTTT
1 T-AATTTTTT
56063474 TAATTTTTT
1 TAATTTTTT
56063483 TAA
1 TAA
56063486 AATAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TAATTTTTT
Found at i:56064272 original size:16 final size:16
Alignment explanation
Indices: 56064247--56064283 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
56064237 TTGTATGGTG
*
56064247 AAATTTAAATTAAAAT
1 AAATTAAAATTAAAAT
56064263 AAATTAAAATTAAAAT
1 AAATTAAAATTAAAAT
56064279 AAATT
1 AAATT
56064284 TATATATAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTAAAATTAAAAT
Found at i:56068440 original size:23 final size:22
Alignment explanation
Indices: 56068388--56068440 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
56068378 TCCACGTCTT
*
56068388 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
56068410 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
56068433 TTTCTTTT
1 TTTCTTTT
56068441 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:56074929 original size:6 final size:6
Alignment explanation
Indices: 56074913--56074963 Score: 66
Period size: 6 Copynumber: 8.3 Consensus size: 6
56074903 TCTAAATGAA
* * *
56074913 TTCATT TCTCATT CTCATT TTCATT TTCATT TTCATT TCCATT TCCATT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TTCATT TTCATT
56074962 TT
1 TT
56074964 GAGAAAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 35 0.88
7 5 0.12
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (6 bp):
TTCATT
Found at i:56078091 original size:22 final size:23
Alignment explanation
Indices: 56078050--56078113 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
56078040 AACAAGATTT
56078050 AATATTAAATTTAATCTAATATA
1 AATATTAAATTTAATCTAATATA
* *
56078073 AATATTATA-TTAATTTAATATTA
1 AATATTAAATTTAATCTAATA-TA
56078096 AAGTGATTAAATTTAATC
1 AA-T-ATTAAATTTAATC
56078114 ATAGTTGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 10 0.30
23 12 0.36
24 1 0.03
25 5 0.15
26 5 0.15
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (23 bp):
AATATTAAATTTAATCTAATATA
Found at i:56085800 original size:20 final size:19
Alignment explanation
Indices: 56085766--56085803 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
56085756 ATTCCAAAAA
*
56085766 TAATATTATTTTAATAATT
1 TAATATTAATTTAATAATT
56085785 TAATATTAAATTTAATAAT
1 TAATATT-AATTTAATAAT
56085804 ACGTATCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATATTAATTTAATAATT
Found at i:56089947 original size:26 final size:26
Alignment explanation
Indices: 56089911--56089987 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
56089901 AAGTATACTG
* *
56089911 TTACTGGCAGCTTTGTTGCGATATTA
1 TTACTGCCAGCTTTGCTGCGATATTA
*
56089937 TTACTGCCAGCTTTGCTGCGATACTA
1 TTACTGCCAGCTTTGCTGCGATATTA
*
56089963 TTACTGCCAGCTTTGCTGTGATATT
1 TTACTGCCAGCTTTGCTGCGATATT
56089988 GGTGTGTTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (26 bp):
TTACTGCCAGCTTTGCTGCGATATTA
Found at i:56090155 original size:33 final size:33
Alignment explanation
Indices: 56090082--56090175 Score: 90
Period size: 33 Copynumber: 3.0 Consensus size: 33
56090072 TGCATTATTG
**
56090082 CACTGTACTAATATTGTATTGGGCTAA-GCCC-
1 CACTGTACTGTTATTGTATTGGGCTAAGGCCCA
* *
56090113 CA---TATTGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTATTGTATTGGGCTAAGGCCCA
* * *
56090143 CACTGTACTGTTATTGAATAGGGCTCAGGCCCA
1 CACTGTACTGTTATTGTATTGGGCTAAGGCCCA
56090176 GATTGTTACT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
28 18 0.37
29 4 0.08
30 2 0.04
31 2 0.04
33 23 0.47
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (33 bp):
CACTGTACTGTTATTGTATTGGGCTAAGGCCCA
Found at i:56090157 original size:28 final size:28
Alignment explanation
Indices: 56090096--56090158 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
56090086 GTACTAATAT
* *
56090096 TGTATTGGGCTAAGCCCCATATTGTTAC
1 TGTATTGGGCTAAGCCCCACACTGTTAC
*
56090124 TGTATTGGGCTAAGGCCCACACTG-TAC
1 TGTATTGGGCTAAGCCCCACACTGTTAC
56090151 TGTTATTG
1 TG-TATTG
56090159 AATAGGGCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (28 bp):
TGTATTGGGCTAAGCCCCACACTGTTAC
Found at i:56094052 original size:20 final size:20
Alignment explanation
Indices: 56094029--56094082 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
56094019 AAAAGTATTG
56094029 ATACCCTTGACAAAGTATCA
1 ATACCCTTGACAAAGTATCA
* ***
56094049 ATACCTTTCTTAAAGTATCA
1 ATACCCTTGACAAAGTATCA
* *
56094069 GTATCCTTGACAAA
1 ATACCCTTGACAAA
56094083 TATTGATACT
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.31
Consensus pattern (20 bp):
ATACCCTTGACAAAGTATCA
Found at i:56094391 original size:35 final size:35
Alignment explanation
Indices: 56094352--56094422 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
56094342 ACACTTACTC
56094352 ACTTAATGTCTCAACAATTCATTTACATTATTCTT
1 ACTTAATGTCTCAACAATTCATTTACATTATTCTT
*
56094387 ACTTAATGTCTCAACAGTTCATTTACATTATTCTT
1 ACTTAATGTCTCAACAATTCATTTACATTATTCTT
56094422 A
1 A
56094423 TGTATTAGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (35 bp):
ACTTAATGTCTCAACAATTCATTTACATTATTCTT
Found at i:56097050 original size:9 final size:9
Alignment explanation
Indices: 56097036--56097067 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
56097026 CTCTGCCAAT
56097036 CTTTTCTCA
1 CTTTTCTCA
56097045 CTTTTCTCA
1 CTTTTCTCA
*
56097054 CCTTTCTCA
1 CTTTTCTCA
56097063 CTTTT
1 CTTTT
56097068 AATTTCTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.09, C:0.34, G:0.00, T:0.56
Consensus pattern (9 bp):
CTTTTCTCA
Found at i:56102891 original size:21 final size:21
Alignment explanation
Indices: 56102866--56102917 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
56102856 GTGGTGGCGG
*
56102866 TGAGATTAGTTACTGTAGCGA
1 TGAGATTAGATACTGTAGCGA
* *
56102887 TGAGATTGGATACTGTAGCGG
1 TGAGATTAGATACTGTAGCGA
56102908 TGAGATTAGA
1 TGAGATTAGA
56102918 AACAATGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (21 bp):
TGAGATTAGATACTGTAGCGA
Found at i:56108743 original size:29 final size:29
Alignment explanation
Indices: 56108701--56108801 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
56108691 CATGAAATTG
56108701 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
56108730 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
56108759 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
56108787 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
56108802 ACTTACTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 19 0.29
29 46 0.71
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:56111418 original size:25 final size:24
Alignment explanation
Indices: 56111379--56111460 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 24
56111369 TCATGTACAT
56111379 GTATGCTCA-TACGAGCTGTGAATTG
1 GTATGCTCACT-CGAGCTGT-AATTG
*
56111404 GTATGCTCACTCGAGCTGTAGATCG
1 GTATGCTCACTCGAGCTGTA-ATTG
* * * *
56111429 GTATGCTCTCACGAGCTATAAATTA
1 GTATGCTCACTCGAGCTGT-AATTG
56111454 GTATGCT
1 GTATGCT
56111461 GACACAAGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 1 0.02
25 45 0.94
26 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (24 bp):
GTATGCTCACTCGAGCTGTAATTG
Found at i:56113314 original size:5 final size:5
Alignment explanation
Indices: 56113300--56113378 Score: 56
Period size: 6 Copynumber: 14.8 Consensus size: 5
56113290 TAAGTCTAGG
*
56113300 AAAAT AAAAAT AAAAT -AACT GAAAAT AAAATT AAAAT AAACAT AAAAATT
1 AAAAT -AAAAT AAAAT AAAAT -AAAAT AAAA-T AAAAT AAA-AT -AAAA-T
56113350 AAAATT AAAAT -AAAT AAAACT AAAA- AAAA
1 AAAA-T AAAAT AAAAT AAAA-T AAAAT AAAA
56113379 CAAGTAAACT
Statistics
Matches: 63, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
4 11 0.17
5 17 0.27
6 31 0.49
7 4 0.06
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:56113349 original size:18 final size:18
Alignment explanation
Indices: 56113321--56113363 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
56113311 AAAATAACTG
56113321 AAAAT-AAAATTAAAA-T
1 AAAATAAAAATTAAAATT
56113337 AAACATAAAAATTAAAATT
1 AAA-ATAAAAATTAAAATT
56113356 AAAATAAA
1 AAAATAAA
56113364 TAAAACTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.12
17 2 0.08
18 15 0.62
19 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATAAAAATTAAAATT
Found at i:56113359 original size:12 final size:11
Alignment explanation
Indices: 56113300--56113363 Score: 67
Period size: 11 Copynumber: 5.7 Consensus size: 11
56113290 TAAGTCTAGG
*
56113300 AAAATAAAAAT
1 AAAATAAAATT
* *
56113311 AAAAT-AACTG
1 AAAATAAAATT
56113321 AAAATAAAATT
1 AAAATAAAATT
*
56113332 AAAATAAACATA
1 AAAATAAA-ATT
56113344 AAAATTAAAATT
1 AAAA-TAAAATT
56113356 AAAATAAA
1 AAAATAAA
56113364 TAAAACTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
10 7 0.16
11 20 0.47
12 12 0.28
13 4 0.09
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (11 bp):
AAAATAAAATT
Found at i:56113363 original size:29 final size:28
Alignment explanation
Indices: 56113321--56113375 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
56113311 AAAATAACTG
56113321 AAAATAAAATTAAA-ATAAACATAAAAATT
1 AAAATAAAATTAAATA-AAAC-TAAAAATT
56113350 AAAATTAAAA-TAAATAAAACTAAAAA
1 AAAA-TAAAATTAAATAAAACTAAAAA
56113376 AAACAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 6 0.25
29 12 0.50
30 6 0.25
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (28 bp):
AAAATAAAATTAAATAAAACTAAAAATT
Found at i:56114778 original size:21 final size:23
Alignment explanation
Indices: 56114753--56114804 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
56114743 CAATGGAAAC
*
56114753 AAATAATAAGT-AG-CAAGAATA
1 AAATAAAAAGTAAGACAAGAATA
*
56114774 AAATAAAAATTAAGACAAGAATA
1 AAATAAAAAGTAAGACAAGAATA
56114797 ATAATAAA
1 A-AATAAA
56114805 TAGATAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 9 0.35
22 2 0.08
23 9 0.35
24 6 0.23
ACGTcount: A:0.67, C:0.04, G:0.10, T:0.19
Consensus pattern (23 bp):
AAATAAAAAGTAAGACAAGAATA
Found at i:56115031 original size:9 final size:9
Alignment explanation
Indices: 56114965--56115068 Score: 65
Period size: 9 Copynumber: 11.9 Consensus size: 9
56114955 AAAATAGTAC
56114965 TAAAATAAA
1 TAAAATAAA
56114974 TAAGAATAAA
1 TAA-AATAAA
*
56114984 -AGTAATAAA
1 TA-AAATAAA
* *
56114993 GAGAATAAA
1 TAAAATAAA
* *
56115002 TGAAATAAT
1 TAAAATAAA
* *
56115011 TAGAAT-AG
1 TAAAATAAA
56115019 TAAAATAAA
1 TAAAATAAA
*
56115028 TAAATTAAA
1 TAAAATAAA
*
56115037 GAAAAT-AA
1 TAAAATAAA
56115045 TAAAAT-AA
1 TAAAATAAA
*
56115053 TAAAAT-GA
1 TAAAATAAA
56115061 TAAAATAA
1 TAAAATAA
56115069 TAAGGAATTA
Statistics
Matches: 73, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
8 28 0.38
9 38 0.52
10 7 0.10
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (9 bp):
TAAAATAAA
Found at i:56115049 original size:8 final size:8
Alignment explanation
Indices: 56115004--56115071 Score: 64
Period size: 8 Copynumber: 8.1 Consensus size: 8
56114994 AGAATAAATG
56115004 AAATAATTA
1 AAATAA-TA
* *
56115013 GAATAGTA
1 AAATAATA
56115021 AAATAAATA
1 AAAT-AATA
* *
56115030 AATTAAAGA
1 AAAT-AATA
56115039 AAATAATA
1 AAATAATA
56115047 AAATAATA
1 AAATAATA
*
56115055 AAATGATA
1 AAATAATA
56115063 AAATAATA
1 AAATAATA
56115071 A
1 A
56115072 GGAATTAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
8 31 0.65
9 17 0.35
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (8 bp):
AAATAATA
Found at i:56123245 original size:28 final size:28
Alignment explanation
Indices: 56123182--56123447 Score: 453
Period size: 28 Copynumber: 9.5 Consensus size: 28
56123172 ATATTAAGTC
*
56123182 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
56123209 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
56123237 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
56123265 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
56123293 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
56123321 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
56123349 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
56123377 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
56123405 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
56123434 CGCACACTTAGTGC
1 CGCACACTTAGTGC
56123448 CAATCTCATG
Statistics
Matches: 228, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
27 22 0.10
28 187 0.82
29 19 0.08
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:56123915 original size:14 final size:14
Alignment explanation
Indices: 56123896--56123925 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56123886 TGGGCATACT
*
56123896 TATGTATATGTATA
1 TATGTATATATATA
56123910 TATGTATATATATA
1 TATGTATATATATA
56123924 TA
1 TA
56123926 CTTCGGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:56128325 original size:42 final size:42
Alignment explanation
Indices: 56128207--56128321 Score: 110
Period size: 41 Copynumber: 2.8 Consensus size: 42
56128197 AACTCGTACA
* * *
56128207 ATGCC-ATATCCCGGATATGGTCTTACATGTTAA-CATATATTG
1 ATGCCAATATCCCAGACATGGTCTTACATG--AATCATATATCG
* * * *
56128249 ATGCCACTATCCCAGACAGGGTCTTATACGAATCATATA-CG
1 ATGCCAATATCCCAGACATGGTCTTACATGAATCATATATCG
* *
56128290 ATGCCAATGTTCCAGACATGGTCTTACATGAA
1 ATGCCAATATCCCAGACATGGTCTTACATGAA
56128322 ATCACACCTT
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
41 29 0.50
42 11 0.19
43 18 0.31
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGCCAATATCCCAGACATGGTCTTACATGAATCATATATCG
Found at i:56128504 original size:31 final size:31
Alignment explanation
Indices: 56128467--56128578 Score: 111
Period size: 31 Copynumber: 3.6 Consensus size: 31
56128457 ATATATATAT
*
56128467 TCATATACGAATCAAATTCGGCAATGAATAT
1 TCATATACGAATCAAATTCGGCAATGAATAA
* * * * *
56128498 TGATATACCAAGC-AATTAGGCAATGTATAA
1 TCATATACGAATCAAATTCGGCAATGAATAA
* * *
56128528 CCATATACGAATCAAGTTTGGCAAT-ATATAA
1 TCATATACGAATCAAATTCGGCAATGA-ATAA
*
56128559 TCATATACAAATCAAATTCG
1 TCATATACGAATCAAATTCG
56128579 ACATCCTATA
Statistics
Matches: 62, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
30 23 0.37
31 39 0.63
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (31 bp):
TCATATACGAATCAAATTCGGCAATGAATAA
Found at i:56128638 original size:31 final size:31
Alignment explanation
Indices: 56128518--56128730 Score: 127
Period size: 31 Copynumber: 6.9 Consensus size: 31
56128508 AGCAATTAGG
* * *
56128518 CAATGTATAACCATATACGAATCAAGTTT-GG
1 CAATGTATAACCATATACAAATTAA-TTTCGA
* * * *
56128549 CAATATATAATCATATACAAATCAAATTCGA
1 CAATGTATAACCATATACAAATTAATTTCGA
* ** *
56128580 C-ATCCTATATTCATAAAC-AATTCAATTTCGA
1 CAAT-GTATAACCATATACAAATT-AATTTCGA
*
56128611 CAATGTATAACCATGTACAAATTAATTTC-A
1 CAATGTATAACCATATACAAATTAATTTCGA
* * * *
56128641 GCAAGGTACAACCATATGCGAATTAA-TTCGGA
1 -CAATGTATAACCATATACAAATTAATTTC-GA
* * *
56128673 -ACT-TATATCCATATAC-AATTCAATTTCAA
1 CAATGTATAACCATATACAAATT-AATTTCGA
* *
56128702 CAATGTATAACCATATAAAAATTATTTTC
1 CAATGTATAACCATATACAAATTAATTTC
56128731 AGCAGTGTTC
Statistics
Matches: 139, Mismatches: 30, Indels: 26
0.71 0.15 0.13
Matches are distributed among these distances:
28 4 0.03
29 13 0.09
30 17 0.12
31 94 0.68
32 11 0.08
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (31 bp):
CAATGTATAACCATATACAAATTAATTTCGA
Found at i:56128813 original size:82 final size:82
Alignment explanation
Indices: 56128676--56128958 Score: 494
Period size: 82 Copynumber: 3.5 Consensus size: 82
56128666 ATTCGGAACT
*
56128676 TATATCCATATACAATTCAATTTCAACAATGTATAACCATATAAAAATTATTTTCAGCAGTGTTC
1 TATATCCATATACAATTCAACTTCAACAATGTATAACCATATAAAAATTATTTTCAGCAGTGTTC
*
56128741 AATCATATACGAATTAA
66 AACCATATACGAATTAA
*
56128758 TATATCCATATACAATTCAACTTCAACAATGTATAACCATATAAAAATTATTTTCAGCACTGTTC
1 TATATCCATATACAATTCAACTTCAACAATGTATAACCATATAAAAATTATTTTCAGCAGTGTTC
*
56128823 AACCATATAAGAATTAA
66 AACCATATACGAATTAA
56128840 TATATCCATATACAATTCAACTTCAACAATGTATAACCATATAAAAATTATTTTCAGCAGTGTTC
1 TATATCCATATACAATTCAACTTCAACAATGTATAACCATATAAAAATTATTTTCAGCAGTGTTC
56128905 AACCATATACGAATTAA
66 AACCATATACGAATTAA
* * * *
56128922 TATATCCATATATAATTAAACTTCGACAATATATAAC
1 TATATCCATATACAATTCAACTTCAACAATGTATAAC
56128959 TATAAACAAT
Statistics
Matches: 191, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 191 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.34
Consensus pattern (82 bp):
TATATCCATATACAATTCAACTTCAACAATGTATAACCATATAAAAATTATTTTCAGCAGTGTTC
AACCATATACGAATTAA
Found at i:56128889 original size:164 final size:168
Alignment explanation
Indices: 56128585--56128958 Score: 531
Period size: 164 Copynumber: 2.2 Consensus size: 168
56128575 TTCGACATCC
* * * * *
56128585 TATATTCATAAACAATTCAATTTCGACAATGTATAACCATGTACAAATTAATTTCAGCAAGGTAC
1 TATATCCATATACAATTCAACTTCGACAATGTATAACCATATAAAAATTAATTTCAGCAAGGTAC
* *
56128650 AACCATATGCGAATTAATTCGGAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCA
66 AACCATAT--GAATGAATT--GAAC-TATATCCATATACAATTCAACTTCAACAATGTATAACCA
*
56128715 TATAAAAATTATTTTCAGCAGTGTTCAATCATATACGAATTAA
126 TATAAAAATTATTTTCAGCAGTGTTCAACCATATACGAATTAA
* * ** *
56128758 TATATCCATATACAATTCAACTTCAACAATGTATAACCATATAAAAATTATTTTCAGCACTGTTC
1 TATATCCATATACAATTCAACTTCGACAATGTATAACCATATAAAAATTAATTTCAGCAAGGTAC
56128823 AACCATAT-AA-GAATT-AA-TATATCCATATACAATTCAACTTCAACAATGTATAACCATATAA
66 AACCATATGAATGAATTGAACTATATCCATATACAATTCAACTTCAACAATGTATAACCATATAA
56128884 AAATTATTTTCAGCAGTGTTCAACCATATACGAATTAA
131 AAATTATTTTCAGCAGTGTTCAACCATATACGAATTAA
* * *
56128922 TATATCCATATATAATTAAACTTCGACAATATATAAC
1 TATATCCATATACAATTCAACTTCGACAATGTATAAC
56128959 TATAAACAAT
Statistics
Matches: 184, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
164 113 0.61
166 2 0.01
169 4 0.02
170 2 0.01
173 63 0.34
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (168 bp):
TATATCCATATACAATTCAACTTCGACAATGTATAACCATATAAAAATTAATTTCAGCAAGGTAC
AACCATATGAATGAATTGAACTATATCCATATACAATTCAACTTCAACAATGTATAACCATATAA
AAATTATTTTCAGCAGTGTTCAACCATATACGAATTAA
Done.