Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1303
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: 33999
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:2928 original size:31 final size:32
Alignment explanation
Indices: 2888--2954 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
2878 TTTTGCAAGA
*
2888 AAAGATTTTTTT-GC-CTTTTTTCCTTAAATTC
1 AAAGATTTTTTTAGCTCATTTTT-CTTAAATTC
* *
2919 AAAGCTTTTTTTATCTCATTTTTCTTAAATTC
1 AAAGATTTTTTTAGCTCATTTTTCTTAAATTC
2951 AAAG
1 AAAG
2955 TCCATCCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 11 0.35
32 14 0.45
33 6 0.19
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (32 bp):
AAAGATTTTTTTAGCTCATTTTTCTTAAATTC
Found at i:4916 original size:23 final size:23
Alignment explanation
Indices: 4874--4938 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
4864 ATCATTCCAA
* *
4874 AAAAAAATCAAAGAAGAAGTTGAC
1 AAAAAAATTAAA-AAAAAGTTGAC
*
4898 AAAAAAATTAAAAAAAAGTTGGC
1 AAAAAAATTAAAAAAAAGTTGAC
*
4921 AAAAAAATTAAAAGAAAG
1 AAAAAAATTAAAAAAAAG
4939 AATCACAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 26 0.70
24 11 0.30
ACGTcount: A:0.68, C:0.05, G:0.14, T:0.14
Consensus pattern (23 bp):
AAAAAAATTAAAAAAAAGTTGAC
Found at i:4947 original size:24 final size:23
Alignment explanation
Indices: 4896--4951 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
4886 GAAGAAGTTG
* *
4896 ACAAAAAAATTAAAAAAAAGTTG
1 ACAAAAAAATTAAAAAAAAGATC
* *
4919 GCAAAAAAATTAAAAGAAAGAATC
1 ACAAAAAAATTAAAAAAAAG-ATC
4943 ACAAAAAAA
1 ACAAAAAAA
4952 ATGGTTGGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.12
Consensus pattern (23 bp):
ACAAAAAAATTAAAAAAAAGATC
Found at i:6412 original size:152 final size:151
Alignment explanation
Indices: 6214--6593 Score: 397
Period size: 152 Copynumber: 2.5 Consensus size: 151
6204 ATGATTTGCT
* * * * * *
6214 TTTGCAAGGAAAGTTTTTCTTTGTCCCATTTTCCTTAAAATCAAAGTTTATTTCTCAAATGAGAT
1 TTTGCAAGAAAAGCTTTTCTTTGACCCATTTTCCTTAAAATAAAAGTTTATCTCTCAAATGAGAC
* * * * ** * *
6279 AAACA-AGGATTCTAG-AATTGGTCTCCATTCCTTTCGTGATTGGGCACTAAAAATTCTCATTGG
66 AAACATA-GATTCTAGTAA-TAGT-TCCATTCCTTTCGAGATTGGGAACCAAAAAGCCCCATTGA
*
6342 GATACATGAAATTGATGGTTTGGC
128 GAGACATGAAATTGATGGTTTGGC
* * *
6366 TTTGTAAGAAAAGCTTTTCTTTGACCTATTTTCCTTAAAATAAAAGTTTATCTCTTAAATGAGAC
1 TTTGCAAGAAAAGCTTTTCTTTGACCCATTTTCCTTAAAATAAAAGTTTATCTCTCAAATGAGAC
* * * * *
6431 AAACATAGATTCTCGTAATAGTTTCATTCTTTTTGAGATTGGGAACCAAAAAGCCCCTTTGAGAG
66 AAACATAGATTCTAGTAATAGTTCCATTCCTTTCGAGATTGGGAACCAAAAAGCCCCATTGAGAG
**
6496 ACATGACTTTGATGGTTTGGC
131 ACATGAAATTGATGGTTTGGC
*** * * * * *
6517 TTTGCAAGAAAAGCTTTTCTACCA-CCATTTTTCATAAAATCAAAGTTCATCTCTTAAATGAGAC
1 TTTGCAAGAAAAGCTTTTCTTTGACCCATTTTCCTTAAAATAAAAGTTTATCTCTCAAATGAGAC
* *
6581 AAATATGGATTCT
66 AAACATAGATTCT
6594 CATCATAATC
Statistics
Matches: 190, Mismatches: 36, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
150 46 0.24
151 70 0.37
152 71 0.37
153 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (151 bp):
TTTGCAAGAAAAGCTTTTCTTTGACCCATTTTCCTTAAAATAAAAGTTTATCTCTCAAATGAGAC
AAACATAGATTCTAGTAATAGTTCCATTCCTTTCGAGATTGGGAACCAAAAAGCCCCATTGAGAG
ACATGAAATTGATGGTTTGGC
Found at i:6532 original size:151 final size:151
Alignment explanation
Indices: 6214--6594 Score: 417
Period size: 151 Copynumber: 2.5 Consensus size: 151
6204 ATGATTTGCT
* * * * * *
6214 TTTGCAAGGAAAGTTTTTCTTTGTCCCATTTTCCTTAAAATCAAAGTTTATTTCTCAAATGAGAT
1 TTTGCAAGAAAAGCTTTTCTTTG-ACCATTTTCCTTAAAATCAAAGTTTATCTCTTAAATGAGAC
* * * * * ** * *
6279 AAACA-AGGATTCTAGAATTGGTCTCCATTCCTTTCGTGATTGGGCACTAAAAATTCTCATTGGG
65 AAACATA-GATTCTCGAATTAGTCTCCATTCCTTTCGAGATTGGGAACCAAAAAGCCCCATTGAG
*
6343 ATACATGAAATTGATGGTTTGGC
129 AGACATGAAATTGATGGTTTGGC
* *
6366 TTTGTAAGAAAAGCTTTTCTTTGACCTATTTTCCTTAAAATAAAAGTTTATCTCTTAAATGAGAC
1 TTTGCAAGAAAAGCTTTTCTTTGACC-ATTTTCCTTAAAATCAAAGTTTATCTCTTAAATGAGAC
* * * *
6431 AAACATAGATTCTCGTAA-TAGT-TTCATTCTTTTTGAGATTGGGAACCAAAAAGCCCCTTTGAG
65 AAACATAGATTCTCG-AATTAGTCTCCATTCCTTTCGAGATTGGGAACCAAAAAGCCCCATTGAG
**
6494 AGACATGACTTTGATGGTTTGGC
129 AGACATGAAATTGATGGTTTGGC
*** * * *
6517 TTTGCAAGAAAAGCTTTTCTACCACCATTTTTCATAAAATCAAAGTTCATCTCTTAAATGAGACA
1 TTTGCAAGAAAAGCTTTTCTTTGACCATTTTCCTTAAAATCAAAGTTTATCTCTTAAATGAGACA
* *
6582 AATATGGATTCTC
66 AACATAGATTCTC
6595 ATCATAATCC
Statistics
Matches: 192, Mismatches: 34, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
150 46 0.24
151 74 0.39
152 69 0.36
153 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (151 bp):
TTTGCAAGAAAAGCTTTTCTTTGACCATTTTCCTTAAAATCAAAGTTTATCTCTTAAATGAGACA
AACATAGATTCTCGAATTAGTCTCCATTCCTTTCGAGATTGGGAACCAAAAAGCCCCATTGAGAG
ACATGAAATTGATGGTTTGGC
Found at i:7495 original size:149 final size:148
Alignment explanation
Indices: 7270--7629 Score: 413
Period size: 148 Copynumber: 2.4 Consensus size: 148
7260 TTTTCCTTAA
* * * * *
7270 AATCAAAGTTTATCCCTCAAATGAGACAAACATGGATTCTTATAATAGTTTCCATTTTTTCATGA
1 AATCAAAG-TTATCTCTTAAATGAGACAAACATGGATTATTATAATAGTCTCCATTCTTTCATGA
* *
7335 CTGAGCACAAAAAATCCTTATT-GGTATGCATGATACTAATGGTTTGGCTTTACAAGGAAAA-C-
65 CTGAGCAC-AAAAATCCTCATTAGG-ATGCATGACACTAATGGTTTGGCTTTAC-AGGAAAAGCT
* * *
7397 TTTTTCCCCCCTATTTTTCGTAG
127 TTTTTACCACC-ATTTTTCATAG
* ** * * * *
7420 AATCAAAGTTAGCTCTTAAATGAGATGAACATGGATTATTGTAATTGTCTCC-TTCTTTCGTGAT
1 AATCAAAGTTATCTCTTAAATGAGACAAACATGGATTATTATAATAGTCTCCATTCTTTCATGAC
* *
7484 TGGGCACCAAAAATCCTCATTAGGATGCATGACAGTAATGGTTTGGCTTTACAGGAAAAGCTTTT
66 TGAGCA-CAAAAATCCTCATTAGGATGCATGACACTAATGGTTTGGCTTTACAGGAAAAGC--TT
7549 TTTTACCACCATTTTTCATAG
128 TTTTACCACCATTTTTCATAG
* * *
7570 AATCAAAGTTCATCTTTTAAATGAGACAAACATGGATTCTTATAATAATCTCCATTCTTT
1 AATCAAAGTT-ATCTCTTAAATGAGACAAACATGGATTATTATAATAGTCTCCATTCTTT
7630 TTAAGATTAG
Statistics
Matches: 175, Mismatches: 27, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
147 7 0.04
148 53 0.30
149 38 0.22
150 28 0.16
151 43 0.25
152 6 0.03
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (148 bp):
AATCAAAGTTATCTCTTAAATGAGACAAACATGGATTATTATAATAGTCTCCATTCTTTCATGAC
TGAGCACAAAAATCCTCATTAGGATGCATGACACTAATGGTTTGGCTTTACAGGAAAAGCTTTTT
TACCACCATTTTTCATAG
Found at i:8066 original size:151 final size:152
Alignment explanation
Indices: 7218--8075 Score: 566
Period size: 151 Copynumber: 5.6 Consensus size: 152
7208 GATACATGTT
* * * * *
7218 ATTAATGATTT-GCTTTTGCAAGGAAAGCTTTTCTTTA--ACTCATTTTCCTTAAAATCAAAGTT
1 ATTAATG-TTTGGC-TTTGCAAGAAAAG-TTTTTTTTACCAC-CATTTTTCATAGAATCAAAGTT
* * * * * * *
7280 TATCCCTCAAATGAGACAAACATGGATTCTTATAATAGTTTCCATT-TTTTCATGACTGAGCACA
62 CATCCCTTAAATGAGACGAACATGGATTCTTGTAATAGTCTCCATTCTTTTCATGATTGGGCACA
* * *
7344 AAAAATCCTTATTG-G-TATGCATGAT
127 AAAAATCCTCATTGAGAT-TACATGAC
* * * * * *
7369 ACTAATGGTTTGGCTTTACAAGGAAAA---CTTTTTCCCCCCTATTTTTCGTAGAATCAAAGTT-
1 ATTAAT-GTTTGGCTTTGCAA-GAAAAGTTTTTTTTACCACC-ATTTTTCATAGAATCAAAGTTC
* * * * * * *
7430 AGCTCTTAAATGAGATGAACATGGATTATTGTAATTGTCTCC-TTC-TTTCGTGATTGGGCACCA
63 ATCCCTTAAATGAGACGAACATGGATTCTTGTAATAGTCTCCATTCTTTTCATGATTGGGCACAA
*
7493 AAAATCCTCATT-AGGA-TGCATGAC
128 AAAATCCTCATTGA-GATTACATGAC
* * *
7517 AGTAATGGTTTGGCTTTACAGGAAAAGCTTTTTTTTACCACCATTTTTCATAGAATCAAAGTTCA
1 ATTAAT-GTTTGGCTTTGCAAGAAAAG-TTTTTTTTACCACCATTTTTCATAGAATCAAAGTTCA
** * * * * * *
7582 TCTTTTAAATGAGACAAACATGGATTCTTATAATAATCTCCATTCTTTTTAAGATTAGGCACCAT
64 TCCCTTAAATGAGACGAACATGGATTCTTGTAATAGTCTCCATTCTTTTCATGATTGGGCA-CA-
* * *
7647 AAACACATTTTTCTCATTAAG-TTACATGAT
127 AAA-A-A---TCCTCATTGAGATTACATGAC
* * * *
7677 ATTGATGCTTTGG-TTTGGCAAG-AAAGCTTTTCTTT-CCACCA-TTTTCTATAGAGGTCTAAGT
1 ATTAATG-TTTGGCTTT-GCAAGAAAAG-TTTTTTTTACCACCATTTTTC-ATAGA-ATCAAAGT
* * * * *** * *
7738 TCGTGCCTCAAATGAGACGAACATTGA-TCTTGTAATAGTCTTTTTTC-TTTCGA-GATTGAGAA
61 TCATCCCTTAAATGAGACGAACATGGATTCTTGTAATAGTCTCCATTCTTTTC-ATGATTGGGCA
* *
7800 TGAAAACTATGTTCCCTTCATTG-GA-TACATGAC
125 -CAAAA--A--AT-CC-TCATTGAGATTACATGAC
* * *
7833 AATAATGCTTT-GATGTTGCAAGAAAAGTTTTTCTTACC-CCTATTTTTCATAGAATCAAAGTTC
1 ATTAATG-TTTGGCT-TTGCAAGAAAAGTTTTTTTTACCACC-ATTTTTCATAGAATCAAAGTTC
* ** *
7896 ATCTCTTAAATGAGTTGAACATGGATTCTTGTAAT-GTCTCCATTCTTTTCATTATTGGGCACAA
63 ATCCCTTAAATGAGACGAACATGGATTCTTGTAATAGTCTCCATTCTTTTCATGATTGGGCACAA
*
7960 AAAATCCTCGTTGAGATTACATGAC
128 AAAATCCTCATTGAGATTACATGAC
* *
7985 ATTAATAGTTTGGCTTTGCAAGAAAAGTTTTTTTTATCACCA-TTTTCATAGAATCAAAGTTTAT
1 ATTAAT-GTTTGGCTTTGCAAGAAAAGTTTTTTTTACCACCATTTTTCATAGAATCAAAGTTCAT
* * *
8049 CCCTTAAATGAGATGAACTTGAATTCT
65 CCCTTAAATGAGACGAACATGGATTCT
8076 CATAATAATC
Statistics
Matches: 548, Mismatches: 109, Indels: 100
0.72 0.14 0.13
Matches are distributed among these distances:
147 5 0.01
148 57 0.10
149 35 0.06
150 44 0.08
151 105 0.19
152 49 0.09
153 16 0.03
154 2 0.00
155 5 0.01
156 74 0.14
157 55 0.10
158 32 0.06
159 42 0.08
160 26 0.05
161 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (152 bp):
ATTAATGTTTGGCTTTGCAAGAAAAGTTTTTTTTACCACCATTTTTCATAGAATCAAAGTTCATC
CCTTAAATGAGACGAACATGGATTCTTGTAATAGTCTCCATTCTTTTCATGATTGGGCACAAAAA
ATCCTCATTGAGATTACATGAC
Found at i:8353 original size:466 final size:465
Alignment explanation
Indices: 7406--8360 Score: 1119
Period size: 466 Copynumber: 2.1 Consensus size: 465
7396 CTTTTTCCCC
*
7406 CCTATTTTTCGTAGAATCAAAGTTAGCTCTTAAATGAGATGAACATGGATTATTGTAATTGTCTC
1 CCTATTTTTCATAGAATCAAAGTTAGCTCTTAAATGAGATGAACATGGATTATTGTAATTGTCTC
* * * *
7471 CTTCTTTCGTGATTGGGCACCAAAAATCCTCATTAGGATGCATGACAGTAATGGTTTGGCTTTAC
66 CTTCTTTCATGATTGGGCACAAAAAATCCTCATTAGGATACATGACAGTAATAGTTTGGCTTTAC
* **
7536 AGGAAAAGCTTTTTTTTACCACCATTTTTCATAGAATCAAAGTTCATCTTTTAAATGAGACAAAC
131 AAGAAAAGCTTTTTTTTACCACCATTTTTCATAGAATCAAAGTTCATCCCTTAAATGAGACAAAC
* * * *
7601 ATGGATTCTTATAATAATCTCCATTCTTTTTAAGATTAGGCACCATAAACACATTTTTCTCATTA
196 ATGAATTCTCATAATAATCTCCATTCTTTTCAAGATTAGGCACCATAAACACATTCTTCTCATTA
** * * *
7666 AGTTACATGATATTGATGCTTTGGTTTGGCAAGAAAGCTTTTCTTTCCACCATTTTCTATAGAGG
261 ACATACATGATATTGATGCTTTGGTTTCGCAAGAAAGCTTTTCTCTCCACCATTTTCAATAGAGG
* * ** ** * *
7731 TCTAAGTTCGTGCCTCAAATGAGACGAACATTGATCTTGTAATAGTCTTTTTTCTTTCGAGATTG
326 TCTAAGTTCGTGCCTCAAATGAGACAAACATGGATCTCATAATAGTCCATTCTCTTTCAAGATTG
** * ** *
7796 AGAATGAAAACTATGTTCCCTTCATTGGATACATGACAATAATGCTTTGATGTTGCAAGAAAAGT
391 AGAACCAAAACTACGTTCCCTTCATTGGATACATGACAATAATGCTTTGATGCCGCAAGAAAAGC
*
7861 TTTTCTTACC
456 TTTTCTTACA
* * *
7871 CCTATTTTTCATAGAATCAAAGTTCATCTCTTAAATGAGTTGAACATGGATTCTTGTAA-TGTCT
1 CCTATTTTTCATAGAATCAAAGTT-AGCTCTTAAATGAGATGAACATGGATTATTGTAATTGTCT
* * *
7935 CCATTCTTTTCATTATTGGGCACAAAAAATCCTCGTT-GAGATTACATGACATTAATAGTTTGGC
65 CC-TTC-TTTCATGATTGGGCACAAAAAATCCTCATTAG-GA-TACATGACAGTAATAGTTTGGC
* * *
7999 TTTGCAAGAAAAG-TTTTTTTTATCACCA-TTTTCATAGAATCAAAGTTTATCCCTTAAATGAGA
126 TTTACAAGAAAAGCTTTTTTTTACCACCATTTTTCATAGAATCAAAGTTCATCCCTTAAATGAGA
** * * *
8062 TGAACTTGAATTCTCATAATAATC-CCAATT-TTGTTCAAGATTAGGTACCATAAACATATTCTT
191 CAAACATGAATTCTCATAATAATCTCC-ATTCTT-TTCAAGATTAGGCACCATAAACACATTCTT
* * * * * *
8125 CTCTTTAACATATATGGTATT-AGTGACTTTGGTTTCGTAGGAAAGACTTTTC-CTCTCACTATT
254 CTCATTAACATACATGATATTGA-TG-CTTTGGTTTCGCAAGAAAG-CTTTTCTCTC-CACCATT
* * *
8188 TTCAATAGA-GT-TTAGTTCGTGCCTCAAATGAGACAAATATGGATTCTCATATTAGTTCCATTC
315 TTCAATAGAGGTCTAAGTTCGTGCCTCAAATGAGACAAACATGGA-TCTCATAATAG-TCCATTC
* * * * *
8251 T-TTTCAAGATTGAGAACCAAAA-TACGTTCCCTTCATTGGGATACATTATAGTGATTCTTTGAT
378 TCTTTCAAGATTGAGAACCAAAACTACGTTCCCTTCATT-GGATACATGACAATAATGCTTTGAT
* *
8314 GCCGTAAGAAAAGCTTTTCTTTTCA
442 GCCGCAAGAAAAGCTTTTC-TTACA
8339 CC-ATTTTT-ATAGAATCAAAGTT
1 CCTATTTTTCATAGAATCAAAGTT
8361 TGTTGCACAA
Statistics
Matches: 413, Mismatches: 62, Indels: 29
0.82 0.12 0.06
Matches are distributed among these distances:
465 35 0.08
466 189 0.46
467 129 0.31
468 60 0.15
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (465 bp):
CCTATTTTTCATAGAATCAAAGTTAGCTCTTAAATGAGATGAACATGGATTATTGTAATTGTCTC
CTTCTTTCATGATTGGGCACAAAAAATCCTCATTAGGATACATGACAGTAATAGTTTGGCTTTAC
AAGAAAAGCTTTTTTTTACCACCATTTTTCATAGAATCAAAGTTCATCCCTTAAATGAGACAAAC
ATGAATTCTCATAATAATCTCCATTCTTTTCAAGATTAGGCACCATAAACACATTCTTCTCATTA
ACATACATGATATTGATGCTTTGGTTTCGCAAGAAAGCTTTTCTCTCCACCATTTTCAATAGAGG
TCTAAGTTCGTGCCTCAAATGAGACAAACATGGATCTCATAATAGTCCATTCTCTTTCAAGATTG
AGAACCAAAACTACGTTCCCTTCATTGGATACATGACAATAATGCTTTGATGCCGCAAGAAAAGC
TTTTCTTACA
Found at i:9353 original size:158 final size:157
Alignment explanation
Indices: 8829--9859 Score: 530
Period size: 158 Copynumber: 6.7 Consensus size: 157
8819 GTATAAGCCC
* * * * *** *
8829 ATGCCTCAAATGAGACAAACAAGGATTCTAGTAACGATCTTTGCTCTTGTCATGATTAGGC-CC-
1 ATGCCTCAAATAAGACAAACATGGATTCTAGTAA-TATCCTCATTCTTTTCATGATTAGGCACCA
* * * *
8892 TATAACACGTTCTAT-TC-TA-GATACATGATATTAATGATTTGCTTT-CACAAGAAAG-CTTTT
65 TA-AACAC-TTCT-TCTCTTAGGATACATGATATTGATGCTTTGGTTTGCATAAGAAAGCCTTTT
* * * * *
8952 CTTTACC-CCATTTTCCTTGAAATCAAAG-TC
127 C-TTACCACCATTTTTCATAAAATCTAAGTTT
* * * * * *
8982 CTCCCTTAAATGAGACAAGA-ATGGATTCTTGTAACAGTAT-C-CATTCTTTTCAAGATTAGGCA
1 ATGCCTCAAATAAGACAA-ACATGGATTCTAGT-A-A-TATCCTCATTCTTTTCATGATTAGGCA
* * * * * *
9044 CCA-AAA-A--TC--CTCATTGGGATACATGACATTGAAGGTTTGACTTTGCA-AGGAAAG-CTT
62 CCATAAACACTTCTTCTC-TTAGGATACATGATATTGATGCTTTG-GTTTGCATAAGAAAGCCTT
* * * *
9101 TT-TTAACACTATTTTTCATAAAATCAAAGTTC
125 TTCTTACCACCATTTTTCATAAAATCTAAGTTT
* * * * *
9133 AT-CTTGAAATGAGGCAAACATGGATTTTCA-TAATAATTCC-CATTCTTTTCATGATTAGGCAC
1 ATGCCTCAAATAAGACAAACATGGATTCT-AGTAAT-A-TCCTCATTCTTTTCATGATTAGGCAC
*
9195 CATAAGCACCTTCTTCTCGTTAGGATACATGATATTGATGCTTTGGTTT-CATAAGAAAGCCTTT
63 CATAAACA-CTTCTTCTC-TTAGGATACATGATATTGATGCTTTGGTTTGCATAAGAAAGCCTTT
** *
9259 TCTT-CCACCATTTTTCATTGAGTCTAAGTTT
126 TCTTACCACCATTTTTCATAAAATCTAAGTTT
* * * *
9290 GTGCCTCAAATAAGACAAACATGGATTCTAGTAGTGA-CTTTCATTCTTTTCATGATTGGGCACC
1 ATGCCTCAAATAAGACAAACATGGATTCTAGTAAT-ATC-CTCATTCTTTTCATGATTAGGCACC
* * * * ** *
9354 ATAAATATGTTCTCCTCTTTAGGATACATGATATTGATGATTTTTTTTGCA-AGGAAAG-CTTTT
64 ATAAACA-CTTCTTCTC-TTAGGATACATGATATTGATGCTTTGGTTTGCATAAGAAAGCCTTTT
* * *
9417 CTTTGCC-TCATTTTTCTTAAAAT-TAAAGTTT
127 C-TTACCACCATTTTTCATAAAATCT-AAGTTT
* * * * *
9448 ATTCCTCAAATGAGACAAACATGGATTTTTGTAATAGT-CTCTATTCTTTTCATGATTAGACACC
1 ATGCCTCAAATAAGACAAACATGGATTCTAGTAATA-TCCTC-ATTCTTTTCATGATTAGGCACC
* * * **
9512 A-AAA-A--TCTTCT-TTGGGATACATGACATTGATGGTTTGGCTTTGGGGT-A-AAAGCCTTTT
64 ATAAACACTTCTTCTCTTAGGATACATGATATTGATGCTTTGG-TTT-GCATAAGAAAGCCTTTT
* * *
9570 -TTACCACTATTTTTCATAAAATCAAAGTTC
127 CTTACCACCATTTTTCATAAAATCTAAGTTT
* * * * *
9600 A--CCTCTTAAATAAAACAAACATGGATTCTCA-TGATAATCCCCATTCCTTTT-AAGAATAGGC
1 ATGCCTC--AAATAAGACAAACATGGATTCT-AGTAAT-ATCCTCATT-CTTTTCATGATTAGGC
* * * * *
9661 ACCATAAACACATTTTTCTCATGAGGATACATGGTATTTATGCTTT--TTT-C-TCAAGAAAGGC
61 ACCATAAACAC-TTCTTCTC-TTAGGATACATGATATTGATGCTTTGGTTTGCAT-AAGAAAGCC
* * * * *
9722 TTTTCTT-CCACTAGTTTTT-GTAGAGTTTAAGTTT
123 TTTTCTTACCACCA-TTTTTCATAAAATCTAAGTTT
* * * * *
9756 ATGCCTTAAATAAGACAAACATGGATTCTAGTAATGATCTTCATTATTTTCAAGATTGGGCACCA
1 ATGCCTCAAATAAGACAAACATGGATTCTAGTAAT-ATCCTCATTCTTTTCATGATTAGGCACCA
* *
9821 TAAACACTT-TTCCTCATTAGG--ACACGATAGTGATGCTTT
65 TAAACACTTCTT-CTC-TTAGGATACATGATATTGATGCTTT
9860 CGTTAAGAAA
Statistics
Matches: 677, Mismatches: 133, Indels: 136
0.72 0.14 0.14
Matches are distributed among these distances:
147 3 0.00
148 2 0.00
149 10 0.01
150 84 0.12
151 46 0.07
152 67 0.10
153 79 0.12
154 8 0.01
155 23 0.03
156 89 0.13
157 77 0.11
158 166 0.25
159 23 0.03
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (157 bp):
ATGCCTCAAATAAGACAAACATGGATTCTAGTAATATCCTCATTCTTTTCATGATTAGGCACCAT
AAACACTTCTTCTCTTAGGATACATGATATTGATGCTTTGGTTTGCATAAGAAAGCCTTTTCTTA
CCACCATTTTTCATAAAATCTAAGTTT
Found at i:9719 original size:466 final size:459
Alignment explanation
Indices: 8404--9966 Score: 1524
Period size: 466 Copynumber: 3.4 Consensus size: 459
8394 AACAATCTCT
* * * *
8404 TTCTTTTCATGATTGGGCACTACAAACACGTTCTCCTTATTGGGATACATGATATTAATGCTTTG
1 TTCTTTTCATGATTGGGCACCATAAACACGTTCTCCTT-TTAGGATACATGATATTAATGATTTG
** *
8469 ACTCACAAGAAGAGCTTTTCTTTGACCTATTTTCCTTAAAATCAAAGTC--CCACTCAAATGAAA
65 -CTTTCAAGAA-AGCTTTTCTTTGACCTATTTTCCTTAAAATCAAAGTCATCC-CTCAAATGAGA
* * **
8532 CAAACATGGATTCTTGCAGTAGTCTCCATTCTTTTGGTGATTAGGCACCAAAAAATCCTCATTGG
127 CAAACATGGATTCTTGTAATAGTCTCCATTCTTTTCATGATTAGGCACC-AAAAATCCTCATTGG
* * * ** * * * *
8597 AATCCATGACATTTATGAATTGGCTTTATAGGGAAAGCTTTTTTTACAACTATTTTTCATAGAAT
191 GATACATGACATTGATGGTTTGGC-TT-TGGGGAAAGCCTTTTTTACCACTATTTTTCATAAAAT
* * * * *
8662 TAAAGTTCA-TCTCCAAATGAGACAAACATTGATTCTCATAATAATCCCCACTT-TTTAAAAAAA
254 CAAAGTTCACTCT-TAAATGAGACAAACATGGATTCTCATAATAATCCCCA-TTCTTT--TAAGA
* * * * ** * *
8725 ATTAGGCACCATAGACATATTCTTCTTATTAGGATATAAAATATTGATGCTTTGGCTTCGCAAGA
315 A-TAGGCACCATAAACACATTCTTCTCATTAGGATACATGATATTGATGCTTT-GTTTCTCAAGA
** * ** * *** * *
8790 AATTCTTTTCATATACCA--TTTCCTGTAGAGTATAAGCCCATGCCTCAAATGAGACAAACAAGG
378 AAGCCTTTTCTTCCACCATTTTTCAT-T-GAGTATAAGTTTATGCCTCAAATAAGACAAACATGG
*
8853 ATTCTAGTAACGATCTTTGC-
441 ATTCTAGTAATGA-CTTT-CA
* * * *
8873 -TCTTGTCATGATTAGGC-CC-TATAACACGTTCT-ATTCTA-GATACATGATATTAATGATTTG
1 TTCTTTTCATGATTGGGCACCATA-AACACGTTCTCCTTTTAGGATACATGATATTAATGATTTG
* * * *
8933 CTTTCACAAGAAAGCTTTTCTTT-ACCCCATTTTCCTTGAAATCAAAGTCCTCCCTTAAATGAGA
65 CTTT--CAAGAAAGCTTTTCTTTGA-CCTATTTTCCTTAAAATCAAAGTCATCCCTCAAATGAGA
* * *
8997 CAAGA-ATGGATTCTTGTAACAGTATCCATTCTTTTCAAGATTAGGCACCAAAAATCCTCATTGG
127 CAA-ACATGGATTCTTGTAATAGTCTCCATTCTTTTCATGATTAGGCACCAAAAATCCTCATTGG
* * * *
9061 GATACATGACATTGAAGGTTTGACTTTGCAAGGAAAG-CTTTTTTAACACTATTTTTCATAAAAT
191 GATACATGACATTGATGGTTTGGCTTTG--GGGAAAGCCTTTTTTACCACTATTTTTCATAAAAT
* * * * *
9125 CAAAGTTCA-TCTTGAAATGAGGCAAACATGGATTTTCATAATAATTCCCATTCTTTTCATGATT
254 CAAAGTTCACTCTT-AAATGAGACAAACATGGATTCTCATAATAATCCCCATTCTTTT-AAGAAT
* * *
9189 AGGCACCATAAGCACCTTCTTCTCGTTAGGATACATGATATTGATGCTTTGGTTTCAT-AAGAAA
317 AGGCACCATAAACACATTCTTCTCATTAGGATACATGATATTGATGCTTT-GTTTC-TCAAGAAA
* *
9253 GCCTTTTCTTCCACCATTTTTCATTGAGTCTAAGTTTGTGCCTCAAATAAGACAAACATGGATTC
380 GCCTTTTCTTCCACCATTTTTCATTGAGTATAAGTTTATGCCTCAAATAAGACAAACATGGATTC
*
9318 TAGTAGTGACTTTCA
445 TAGTAATGACTTTCA
* * * *
9333 TTCTTTTCATGATTGGGCACCATAAATATGTTCTCCTCTTTAGGATACATGATATTGATGATTTT
1 TTCTTTTCATGATTGGGCACCATAAACACGTTCTCCT-TTTAGGATACATGATATTAATGATTTG
* * * * *
9398 TTTTGCAAGGAAAGCTTTTCTTTG-CCTCATTTTTCTTAAAATTAAAGTTTATTCCTCAAATGAG
65 CTTT-CAA-GAAAGCTTTTCTTTGACCT-ATTTTCCTTAAAATCAAAG-TCATCCCTCAAATGAG
* * * * *
9462 ACAAACATGGATTTTTGTAATAGTCTCTATTCTTTTCATGATTAGACACCAAAAATCTTCTTTGG
126 ACAAACATGGATTCTTGTAATAGTCTCCATTCTTTTCATGATTAGGCACCAAAAATCCTCATTGG
9527 GATACATGACATTGATGGTTTGGCTTTGGGGTAAAAGCCTTTTTTACCACTATTTTTCATAAAAT
191 GATACATGACATTGATGGTTTGGCTTTGGGG--AAAGCCTTTTTTACCACTATTTTTCATAAAAT
* * *
9592 CAAAGTTCACCTCTTAAATAAAACAAACATGGATTCTCATGATAATCCCCATTCCTTTTAAGAAT
254 CAAAGTTCA-CTCTTAAATGAGACAAACATGGATTCTCATAATAATCCCCATT-CTTTTAAGAAT
* * * * *
9657 AGGCACCATAAACACATTTTTCTCATGAGGATACATGGTATTTATGCTTT-TTTCTCAAGAAAGG
317 AGGCACCATAAACACATTCTTCTCATTAGGATACATGATATTGATGCTTTGTTTCTCAAGAAAGC
* * * * *
9721 CTTTTCTTCCACTAGTTTTT-GTAGAGTTTAAGTTTATGCCTTAAATAAGACAAACATGGATTCT
382 CTTTTCTTCCACCA-TTTTTCATTGAGTATAAGTTTATGCCTCAAATAAGACAAACATGGATTCT
9785 AGTAATGA-TCTTCA
446 AGTAATGACT-TTCA
* * * * * * * *
9799 TTATTTTCAAGATTGGGCACCATAAACAC-TTTTCCTCATTAGG--ACACGATAGTGATGCTTT-
1 TTCTTTTCATGATTGGGCACCATAAACACGTTCTCCT-TTTAGGATACATGATATTAATGATTTG
* * ** *
9860 CGTT-AAGAAAGCTTTTCTTTGTCCTATTTTCCTTAAAATCAAAGTTCATTACTTAAATGAGACA
65 CTTTCAAGAAAGCTTTTCTTTGACCTATTTTCCTTAAAATCAAAG-TCATCCCTCAAATGAGACA
* ** *
9924 AACATAGATTCTCATAATAGTCTCTATTCTTTTCGA-GATTAGG
129 AACATGGATTCTTGTAATAGTCTCCATTCTTTTC-ATGATTAGG
9967 AATAAAAAAT
Statistics
Matches: 912, Mismatches: 144, Indels: 86
0.80 0.13 0.08
Matches are distributed among these distances:
459 86 0.09
460 10 0.01
461 119 0.13
462 18 0.02
463 97 0.11
464 102 0.11
465 124 0.14
466 202 0.22
467 51 0.06
468 94 0.10
469 9 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (459 bp):
TTCTTTTCATGATTGGGCACCATAAACACGTTCTCCTTTTAGGATACATGATATTAATGATTTGC
TTTCAAGAAAGCTTTTCTTTGACCTATTTTCCTTAAAATCAAAGTCATCCCTCAAATGAGACAAA
CATGGATTCTTGTAATAGTCTCCATTCTTTTCATGATTAGGCACCAAAAATCCTCATTGGGATAC
ATGACATTGATGGTTTGGCTTTGGGGAAAGCCTTTTTTACCACTATTTTTCATAAAATCAAAGTT
CACTCTTAAATGAGACAAACATGGATTCTCATAATAATCCCCATTCTTTTAAGAATAGGCACCAT
AAACACATTCTTCTCATTAGGATACATGATATTGATGCTTTGTTTCTCAAGAAAGCCTTTTCTTC
CACCATTTTTCATTGAGTATAAGTTTATGCCTCAAATAAGACAAACATGGATTCTAGTAATGACT
TTCA
Found at i:13146 original size:81 final size:79
Alignment explanation
Indices: 13009--13282 Score: 276
Period size: 77 Copynumber: 3.5 Consensus size: 79
12999 TTCACCATTG
* * * * **
13009 GGGATACTCCAACCTCGTGTTTACTTCCTAAATATC-AAATGTTTCACCATCAGGGATACTCCAA
1 GGGATACTCCAACCCCATTTTTACTTCCAAAATATCAAAAT-TTTCA-CATTGGGGATACTCCAA
*
13073 TCC-CATTATTTTTGAA
64 -CCTCATTATTTATGAA
*
13089 GGGATACTCTAACCCCATTTTTACTTCCAAAAATATCAAAATTTTCACTATTGGGGATACTCCAA
1 GGGATACTCCAACCCCATTTTTACTTCC-AAAATATCAAAATTTTCAC-ATTGGGGATACTCCAA
*
13154 CCTCATTATTTATGAG
64 CCTCATTATTTATGAA
* * * *
13170 GGGATACT----CCCCGTTTCTACTTCCAAAAATATCAAATATTTTGC-CATTGCGGTTACTCCA
1 GGGATACTCCAACCCCATTTTTACTTCC-AAAATATCAAA-ATTTT-CACATTGGGGATACTCCA
* *
13230 ACCTTATCATTTATGAA
63 ACCTCATTATTTATGAA
13247 GGGATACTCCAACCCCATTTTTA-TCTCCAAAATATC
1 GGGATACTCCAACCCCATTTTTACT-TCCAAAATATC
13283 GAATACTTCA
Statistics
Matches: 165, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
77 61 0.37
78 6 0.04
79 1 0.01
80 36 0.22
81 57 0.35
82 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (79 bp):
GGGATACTCCAACCCCATTTTTACTTCCAAAATATCAAAATTTTCACATTGGGGATACTCCAACC
TCATTATTTATGAA
Found at i:14092 original size:19 final size:20
Alignment explanation
Indices: 14054--14092 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
14044 ATAGGCATCC
*
14054 GATCATGCCTAACTCGAAAT
1 GATCATGCCTAACTCCAAAT
*
14074 GATCATGGC-AACTCCAAAT
1 GATCATGCCTAACTCCAAAT
14093 TCATAGTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (20 bp):
GATCATGCCTAACTCCAAAT
Found at i:18160 original size:620 final size:619
Alignment explanation
Indices: 16804--18160 Score: 1353
Period size: 620 Copynumber: 2.2 Consensus size: 619
16794 AAGGAAAATG
* * * *
16804 TGGT-GAAA-AAAAGC-TTTCTTTGCGAA-AGCAAATCATCAATAT-TGTGTATCCAAATGAGGA
1 TGGTGGAAAGAAAAGCTTTTC-TTGC-AACACCAAAACATCAATATCT-TGTATCCCAATGA-AA
* * * * * *
16864 A-AACGTGTTTATGGTGCCTAATCATGAAAAGATTGAAGATCATTACTAGAATCCATATTTGTCT
62 AGAACGTGTTTATGGTGCCCAATTACGAAAAGAATGAAGATCATTACCAGAATCAATATTTGTCT
* * * * *
16928 -AA----T-T-TAAGGCACGAACTTAGACTTTTAT-GAAA--ATG-GTGGAAGAAAAACCTTTCT
127 AAATGTTTGTCTGAGGAATGAACTTAGAC-TCTATGGAAAGCA-GAG-GGAAAAAAAACCTTTCT
* * * * *
16982 TGCGAAACTAAAACATCAATATCATGTATCCTAGTGAGAATAATGTGTTTATGGTGCCTAATCTT
189 TACAAAACTAAAACATCAATATCATGTATCCTAATGAGAAGAATGTGTTTATGGTGCCCAATCTT
* * *
17047 GCAAAGAATAGAGATTATGAGAATCGATGTTTGTCTCATTTAAGAGACTTTGACTATGAAAAATG
254 GCAAAGAATAGAGATTATAAAAATCGATGTTTGTCTCATTTAAGAGACTTTAACTATGAAAAATG
* * * ***
17112 GTGGTAAAAAAAGCTTTCTTGTAAAGCCAAGCCATCAATGTCATGTATCCCATTTTGGATTTTTG
319 GTGGTAAAAAAAGCTTTCTTGCAAAGCCAAACCATCAATGTCATGTATCCCAATAAAGATTTTTG
* * * * * *
17177 GTGTCCGATCATAAAAACAATGGAGATAACAAGAATCCATGTTTGTCTCATTTGAGGGACGAAGT
384 GTATCCAATCATAAAAACAATGGAGATAACAAGAATCCATGTTTGTCTCATTTGAAGAACAAACT
* * * *
17242 CTGATTTTAAGGAAAATGTGTTAAACAAAAGCTTTCTTAAGAAATCAAAACGCCAATATCATGTA
449 CTAATTTTAAGGAAAATATGTCAAACAAAAGCTTTCTTAAGAAAGCAAAACGCC-ATATCATGTA
* * *
17307 TCCTAATAAGGAGAACTTGTTTTTGGTGCCCAATCATGAATAGATGGAGATCGTTATAACAATCC
513 T-CTAATAAGGAGAACTTGTTTATGGTACCCAATCATGAATAGATGGAGATCGTTACAACAATCC
* * * * *
17372 AACTTTGTTTCATTTGGAAGATAAACTTTAATTCTATCAAAAG
577 AACTATGTCTCAATTGGAAGATAAACTTTAATTCCATCAAAAA
* * * *
17415 TGGTGGAAGGAAATGCTTTTCTTGCAACACTAAAACATCAATATCTTGTATCCTAATGAAAAGAA
1 TGGTGGAAAGAAAAGCTTTTCTTGCAACACCAAAACATCAATATCTTGTATCCCAATGAAAAGAA
* * * * *
17480 TGTGTTTATGGTGCCCAATTATGAAAAGAATTAAGATCATTACCATAATCAATGTTTGTCTAAAT
66 CGTGTTTATGGTGCCCAATTACGAAAAGAATGAAGATCATTACCAGAATCAATATTTGTCTAAAT
17545 GTTTGTCTGAGGAATGAACTTAGACTCTATGGAAAGCAGAGGGAAAAAAAACCTTTCTTACAAAA
131 GTTTGTCTGAGGAATGAACTTAGACTCTATGGAAAGCAGAGGGAAAAAAAACCTTTCTTACAAAA
* * *
17610 CTAAAGCATCAATATCGTGTATCTTAATGA-AAGAATGTGTTTATGGTGCCCAATCTTG-AAAGA
196 CTAAAACATCAATATCATGTATCCTAATGAGAAGAATGTGTTTATGGTGCCCAATCTTGCAAAGA
* * * *
17673 ATGGGGACTACTATAAAAATCTATGTTTGTCTCATTTAAGAGGCTAACTTTAATTTTATGAAAAA
261 ATAGAGA-T--TATAAAAATCGATGTTTGTCTCATTTAAGA-G---ACTTTAA--CTATGAAAAA
*
17738 TGGTGGTAAAAAAAGCTTTCCTTGCAAAGCCAAACCATCAATGTCATGTATCCTAATAAAGATTT
317 TGGTGGTAAAAAAAGCTTT-CTTGCAAAGCCAAACCATCAATGTCATGTATCCCAATAAAGATTT
* * * * *
17803 TTGGTATGCAATCATGAAAAA-TATGGTGGCT-ACAAGAATCCATGTTTGTCTCATTTGAAGAAT
381 TTGGTATCCAATCAT-AAAAACAATGG-AGATAACAAGAATCCATGTTTGTCTCATTTGAAGAAC
* * ** *
17866 AAACTTTAATTTTAAGGAAAATATGTCAAAGAAAAGCTTTTTCTTGTG-AAGCCAAA-G-C-T-T
444 AAACTCTAATTTTAAGGAAAATATGTCAAACAAAAGC--TTTCTTAAGAAAGCAAAACGCCATAT
* * * * *
17926 CA-GTAT-TGATGAGGAGAA-TGTGTTTATGGTACCCAATCATTAA-AGATGGAGATTGTTACGA
507 CATGTATCTAATAAGGAGAACT-TGTTTATGGTACCCAATCATGAATAGATGGAGATCGTTACAA
* * *
17987 TAATCCAAGTATGTCT-AATT-GAGAGATAAACTTTGATTCCATCAAAAA
571 CAATCCAACTATGTCTCAATTGGA-AGATAAACTTTAATTCCATCAAAAA
* ** * * * *
18035 TGGTGGAAAGAAAAGTTTTTCTTGTGACACCAAAGCATCACTGT-TATGTATCCCAATGAAAGGA
1 TGGTGGAAAGAAAAGCTTTTCTTGCAACACCAAAACATCAATATCT-TGTATCCCAATGAAAAGA
* * * * ** *
18099 ACGTGTTTTTGGTTCCCAATCT-CGATAAGAATGGAGA-CTATTAGGAGAATCCATATTTGTCT
65 ACGTGTTTATGGTGCCCAAT-TACGAAAAGAATGAAGATC-ATTACCAGAATCAATATTTGTCT
18161 CATTTAAGGG
Statistics
Matches: 608, Mismatches: 102, Indels: 63
0.79 0.13 0.08
Matches are distributed among these distances:
611 4 0.01
612 7 0.01
613 88 0.14
614 7 0.01
618 1 0.00
619 19 0.03
620 168 0.28
621 77 0.13
622 59 0.10
623 1 0.00
624 4 0.01
625 3 0.00
626 7 0.01
628 29 0.05
629 114 0.19
630 13 0.02
631 7 0.01
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (619 bp):
TGGTGGAAAGAAAAGCTTTTCTTGCAACACCAAAACATCAATATCTTGTATCCCAATGAAAAGAA
CGTGTTTATGGTGCCCAATTACGAAAAGAATGAAGATCATTACCAGAATCAATATTTGTCTAAAT
GTTTGTCTGAGGAATGAACTTAGACTCTATGGAAAGCAGAGGGAAAAAAAACCTTTCTTACAAAA
CTAAAACATCAATATCATGTATCCTAATGAGAAGAATGTGTTTATGGTGCCCAATCTTGCAAAGA
ATAGAGATTATAAAAATCGATGTTTGTCTCATTTAAGAGACTTTAACTATGAAAAATGGTGGTAA
AAAAAGCTTTCTTGCAAAGCCAAACCATCAATGTCATGTATCCCAATAAAGATTTTTGGTATCCA
ATCATAAAAACAATGGAGATAACAAGAATCCATGTTTGTCTCATTTGAAGAACAAACTCTAATTT
TAAGGAAAATATGTCAAACAAAAGCTTTCTTAAGAAAGCAAAACGCCATATCATGTATCTAATAA
GGAGAACTTGTTTATGGTACCCAATCATGAATAGATGGAGATCGTTACAACAATCCAACTATGTC
TCAATTGGAAGATAAACTTTAATTCCATCAAAAA
Found at i:19672 original size:13 final size:13
Alignment explanation
Indices: 19654--19679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19644 TATTAAAAAT
19654 TATTTTATATTAA
1 TATTTTATATTAA
19667 TATTTTATATTAA
1 TATTTTATATTAA
19680 AAATTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTATATTAA
Found at i:19905 original size:22 final size:22
Alignment explanation
Indices: 19880--19940 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
19870 TGATATTTAA
19880 TAATTAACAAATTATTTAAAT-T
1 TAATTAA-AAATTATTTAAATAT
*
19902 TAATTATAAAA-TATATAAATAT
1 TAATTA-AAAATTATTTAAATAT
19924 TAATATAAAAATTATTT
1 TAAT-TAAAAATTATTT
19941 TTAATTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 8 0.24
22 18 0.55
23 7 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATTAAAAATTATTTAAATAT
Found at i:24650 original size:14 final size:15
Alignment explanation
Indices: 24631--24659 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24621 TTTCAAGTGC
24631 CTTTTT-GCCAAGTT
1 CTTTTTAGCCAAGTT
24645 CTTTTTAGCCAAGTT
1 CTTTTTAGCCAAGTT
24660 TGTAGCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (15 bp):
CTTTTTAGCCAAGTT
Found at i:30987 original size:18 final size:18
Alignment explanation
Indices: 30966--31016 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
30956 TATTAATCTC
*
30966 TTAATATTAT-ATAATAT
1 TTAATATTATAATAAAAT
*
30983 ATTAAAATTATAATAAAAT
1 -TTAATATTATAATAAAAT
31002 TTAATA--ATAATAAAA
1 TTAATATTATAATAAAA
31017 ATAATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.31
18 14 0.48
19 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAATATTATAATAAAAT
Found at i:32435 original size:14 final size:15
Alignment explanation
Indices: 32395--32435 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
32385 AAAAAACATT
32395 ATATTATAAATATGA
1 ATATTATAAATATGA
**
32410 ATATT-TTTATATGA
1 ATATTATAAATATGA
32424 A-ATTATAAATAT
1 ATATTATAAATAT
32436 ACAAAATAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
13 3 0.14
14 13 0.62
15 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (15 bp):
ATATTATAAATATGA
Found at i:33000 original size:22 final size:22
Alignment explanation
Indices: 32975--33018 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
32965 AATTTAATAA
*
32975 ATAATTTTAA-AAATATTTTTAT
1 ATAAATTTAATAAA-ATTTTTAT
32997 ATAAATTTAATAAAATTTTTAT
1 ATAAATTTAATAAAATTTTTAT
33019 TTTTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAAATTTAATAAAATTTTTAT
Done.